From paulg at email.unc.edu  Wed Jul  2 13:41:43 2008
From: paulg at email.unc.edu (Paul Giresi)
Date: Wed, 02 Jul 2008 16:41:43 -0400
Subject: [Genome-mirror] missing html code
Message-ID: <486BE807.8080303@email.unc.edu>

I recently installed a local version of the UCSC genome browser and 
everything seemed to have gone smoothly the only issue I am having is a 
small bit of html is missing in my installation (see below)  I've 
highlighted the portion that is present in the UCSC version but not this 
local version ( width='100*_%'_* ), which results in the names of the 
groups not being displayed (such as "Mapping and Sequencing Tracks").

I don't think this is the result of anything I did, but if so I would 
obviously like to correct this problem.

I installed the browser on an Intel Mac Pro running Mac OS X 10.5 
(Leopard).  Any suggestions for how to correct the problem or clues as 
to what script may be generating this error would be much appreciated.


My browser installation:

<A NAME="userGroup"></A><A 
HREF="../cgi-bin/hgTracks?hgsid=106&hgtgroup_user_close=1#userGroup" 
class='bigBlue'><IMG height='18' width='18' onclick="return 
toggleTrackGroupVisibility(this, 'user');" id="user_button" 
src="../images/remove_sm.gif" alt="-" 
class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' width='100>
<B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>

UCSC browser installation:

<A NAME="userGroup"></A><A 
HREF="../cgi-bin/hgTracks?hgsid=109243755&hgtgroup_user_close=1#userGroup" 
class='bigBlue'><IMG height='18' width='18' onclick="return 
toggleTrackGroupVisibility(this, 'user');" id="user_button" 
src="../images/remove_sm.gif" alt="-" 
class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' width='100*_%'_*>
<B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>

Paul

-- 
================================
Paul Giresi

Graduate Student
Lieb Lab
Department of Biology
University of North Carolina at Chapel Hill
407 Fordham Hall, CB#3280
Chapel Hill, NC 27599
919-843-3229
================================


From ann at soe.ucsc.edu  Wed Jul  2 16:05:08 2008
From: ann at soe.ucsc.edu (Ann Zweig)
Date: Wed, 02 Jul 2008 16:05:08 -0700
Subject: [Genome-mirror] missing html code
In-Reply-To: <486BE807.8080303@email.unc.edu>
References: <486BE807.8080303@email.unc.edu>
Message-ID: <486C09A4.4050504@soe.ucsc.edu>

Hello Paul,

	This is a known bug which we believe that we have recently 
fixed.  The code that supports this fix will be released to 
the public website and the mirror download area July 11.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


Paul Giresi wrote:
> I recently installed a local version of the UCSC genome browser and 
> everything seemed to have gone smoothly the only issue I am having is a 
> small bit of html is missing in my installation (see below)  I've 
> highlighted the portion that is present in the UCSC version but not this 
> local version ( width='100*_%'_* ), which results in the names of the 
> groups not being displayed (such as "Mapping and Sequencing Tracks").
> 
> I don't think this is the result of anything I did, but if so I would 
> obviously like to correct this problem.
> 
> I installed the browser on an Intel Mac Pro running Mac OS X 10.5 
> (Leopard).  Any suggestions for how to correct the problem or clues as 
> to what script may be generating this error would be much appreciated.
> 
> 
> My browser installation:
> 
> <A NAME="userGroup"></A><A 
> HREF="../cgi-bin/hgTracks?hgsid=106&hgtgroup_user_close=1#userGroup" 
> class='bigBlue'><IMG height='18' width='18' onclick="return 
> toggleTrackGroupVisibility(this, 'user');" id="user_button" 
> src="../images/remove_sm.gif" alt="-" 
> class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' width='100>
> <B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>
> 
> UCSC browser installation:
> 
> <A NAME="userGroup"></A><A 
> HREF="../cgi-bin/hgTracks?hgsid=109243755&hgtgroup_user_close=1#userGroup" 
> class='bigBlue'><IMG height='18' width='18' onclick="return 
> toggleTrackGroupVisibility(this, 'user');" id="user_button" 
> src="../images/remove_sm.gif" alt="-" 
> class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' width='100*_%'_*>
> <B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>
> 
> Paul
> 

From paulg at email.unc.edu  Wed Jul  2 16:14:34 2008
From: paulg at email.unc.edu (Paul Giresi)
Date: Wed, 02 Jul 2008 19:14:34 -0400
Subject: [Genome-mirror] missing html code
In-Reply-To: <486C09A4.4050504@soe.ucsc.edu>
References: <486BE807.8080303@email.unc.edu> <486C09A4.4050504@soe.ucsc.edu>
Message-ID: <486C0BDA.2050209@email.unc.edu>

Thank you, I'll look forward to the fix.

Will I be able to obtain the necessary fix by rsync'ing with the cgi-bin 
directory? 

Paul

Ann Zweig wrote:
> Hello Paul,
>
>     This is a known bug which we believe that we have recently fixed.  
> The code that supports this fix will be released to the public website 
> and the mirror download area July 11.
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
> Paul Giresi wrote:
>> I recently installed a local version of the UCSC genome browser and 
>> everything seemed to have gone smoothly the only issue I am having is 
>> a small bit of html is missing in my installation (see below)  I've 
>> highlighted the portion that is present in the UCSC version but not 
>> this local version ( width='100*_%'_* ), which results in the names 
>> of the groups not being displayed (such as "Mapping and Sequencing 
>> Tracks").
>>
>> I don't think this is the result of anything I did, but if so I would 
>> obviously like to correct this problem.
>>
>> I installed the browser on an Intel Mac Pro running Mac OS X 10.5 
>> (Leopard).  Any suggestions for how to correct the problem or clues 
>> as to what script may be generating this error would be much 
>> appreciated.
>>
>>
>> My browser installation:
>>
>> <A NAME="userGroup"></A><A 
>> HREF="../cgi-bin/hgTracks?hgsid=106&hgtgroup_user_close=1#userGroup" 
>> class='bigBlue'><IMG height='18' width='18' onclick="return 
>> toggleTrackGroupVisibility(this, 'user');" id="user_button" 
>> src="../images/remove_sm.gif" alt="-" 
>> class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' width='100>
>> <B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>
>>
>> UCSC browser installation:
>>
>> <A NAME="userGroup"></A><A 
>> HREF="../cgi-bin/hgTracks?hgsid=109243755&hgtgroup_user_close=1#userGroup" 
>> class='bigBlue'><IMG height='18' width='18' onclick="return 
>> toggleTrackGroupVisibility(this, 'user');" id="user_button" 
>> src="../images/remove_sm.gif" alt="-" 
>> class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' 
>> width='100*_%'_*>
>> <B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>
>>
>> Paul
>>
>

From ann at soe.ucsc.edu  Wed Jul  2 16:36:19 2008
From: ann at soe.ucsc.edu (Ann Zweig)
Date: Wed, 02 Jul 2008 16:36:19 -0700
Subject: [Genome-mirror] missing html code
In-Reply-To: <486C0BDA.2050209@email.unc.edu>
References: <486BE807.8080303@email.unc.edu> <486C09A4.4050504@soe.ucsc.edu>
	<486C0BDA.2050209@email.unc.edu>
Message-ID: <486C10F3.5060301@soe.ucsc.edu>

Hi Paul,

	You can either wait until July 11 and get the 
code-reviewed, quality-checked, zipped source code.  Or, you 
can check out the source tree and build it yourself with 
whatever happens to be in the tree at the time you get the 
code.  If you choose to do that, you can follow the 
instructions here: 
http://genome.ucsc.edu/admin/mirror.html#step6

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Paul Giresi wrote:
> Thank you, I'll look forward to the fix.
> 
> Will I be able to obtain the necessary fix by rsync'ing with the cgi-bin 
> directory?
> Paul
> 
> Ann Zweig wrote:
>> Hello Paul,
>>
>>     This is a known bug which we believe that we have recently fixed.  
>> The code that supports this fix will be released to the public website 
>> and the mirror download area July 11.
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>> Paul Giresi wrote:
>>> I recently installed a local version of the UCSC genome browser and 
>>> everything seemed to have gone smoothly the only issue I am having is 
>>> a small bit of html is missing in my installation (see below)  I've 
>>> highlighted the portion that is present in the UCSC version but not 
>>> this local version ( width='100*_%'_* ), which results in the names 
>>> of the groups not being displayed (such as "Mapping and Sequencing 
>>> Tracks").
>>>
>>> I don't think this is the result of anything I did, but if so I would 
>>> obviously like to correct this problem.
>>>
>>> I installed the browser on an Intel Mac Pro running Mac OS X 10.5 
>>> (Leopard).  Any suggestions for how to correct the problem or clues 
>>> as to what script may be generating this error would be much 
>>> appreciated.
>>>
>>>
>>> My browser installation:
>>>
>>> <A NAME="userGroup"></A><A 
>>> HREF="../cgi-bin/hgTracks?hgsid=106&hgtgroup_user_close=1#userGroup" 
>>> class='bigBlue'><IMG height='18' width='18' onclick="return 
>>> toggleTrackGroupVisibility(this, 'user');" id="user_button" 
>>> src="../images/remove_sm.gif" alt="-" 
>>> class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' width='100>
>>> <B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>
>>>
>>> UCSC browser installation:
>>>
>>> <A NAME="userGroup"></A><A 
>>> HREF="../cgi-bin/hgTracks?hgsid=109243755&hgtgroup_user_close=1#userGroup" 
>>> class='bigBlue'><IMG height='18' width='18' onclick="return 
>>> toggleTrackGroupVisibility(this, 'user');" id="user_button" 
>>> src="../images/remove_sm.gif" alt="-" 
>>> class='bigBlue'></A>&nbsp;&nbsp;</td><td align='center' 
>>> width='100*_%'_*>
>>> <B><FONT COLOR="#FFFFFF">Custom Tracks</FONT></B></td><td align='right'>
>>>
>>> Paul
>>>
>>

From rhead at soe.ucsc.edu  Thu Jul  3 12:36:59 2008
From: rhead at soe.ucsc.edu (Brooke Rhead)
Date: Thu, 03 Jul 2008 12:36:59 -0700
Subject: [Genome-mirror] notice of large data release: 60 GB
Message-ID: <486D2A5B.4090806@soe.ucsc.edu>

Hello mirror sites,

On Monday, there will be an additional 8 GB of files added to /gbdb:

/gbdb/hgFixed/transMap/vertebrate.2008-06-07/mrna.fa
/gbdb/hgFixed/transMap/vertebrate.2008-06-07/refSeq.fa
/gbdb/hgFixed/transMap/vertebrate.2008-06-07/splicedEst.fa
/gbdb/hgFixed/transMap/vertebrate.2008-06-07/ucscGenes.fa

This is in preparation for a new set of tracks called TransMap. 
TransMap is an alignment of cDNAs and genes across all vertebrates in 
the Genome Browser.

When it is released, there will be additional tables in the following 
databases: hgFixed anoCar1 bosTau4 calJac1 canFam2 cavPor3 danRer5 
equCab2 felCat3 fr2 galGal3 gasAcu1 hg18 mm9 monDom4 ornAna1 oryLat1 
panTro2 petMar1 ponAbe2 rheMac2 rn4 tetNig1 xenTro2.

In total, there will be ~60 GB of new data to support these tracks.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

From m.wittig at mucosa.de  Sun Jul  6 11:06:06 2008
From: m.wittig at mucosa.de (Michael Wittig)
Date: Sun, 06 Jul 2008 20:06:06 +0200
Subject: [Genome-mirror] customTrash table
Message-ID: <4871098E.8090302@mucosa.de>

Hi,

I spend this weekend installing a local genome browser and got it 
running. Finally to add custom tracks I setted up the customTrash 
database but where can I find the metaInfo and history table. Or the sql 
create statements. I can't find them ...

thanks and best regards,
michael

From hiram at soe.ucsc.edu  Sun Jul  6 13:46:14 2008
From: hiram at soe.ucsc.edu (Hiram Clawson)
Date: Sun, 06 Jul 2008 13:46:14 -0700
Subject: [Genome-mirror] customTrash table
In-Reply-To: <4871098E.8090302@mucosa.de>
References: <4871098E.8090302@mucosa.de>
Message-ID: <48712F16.1090700@soe.ucsc.edu>

Good Afternoon Michael:

Those tables are created by the loaders as tracks are loaded.
You do not need to create them.  Did you find the instructions
on setting up the database ?
http://genomewiki.ucsc.edu/index.php/Using_custom_track_database

--Hiram

Michael Wittig wrote:
> Hi,
> 
> I spend this weekend installing a local genome browser and got it 
> running. Finally to add custom tracks I setted up the customTrash 
> database but where can I find the metaInfo and history table. Or the sql 
> create statements. I can't find them ...
> 
> thanks and best regards,
> michael

From davide.cittaro at ifom-ieo-campus.it  Mon Jul  7 06:01:47 2008
From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro)
Date: Mon, 7 Jul 2008 15:01:47 +0200
Subject: [Genome-mirror] hgdownload down?
Message-ID: <C3B1193A-6C71-416B-963A-227A3AAAA2C3@ifom-ieo-campus.it>

Hi all, is hgdownload.cse.ucsc.edu ok? I cannot even ping it... :-(

Thanks

d


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro at ifom-ieo-campus.it
*/




From ann at soe.ucsc.edu  Mon Jul  7 09:06:06 2008
From: ann at soe.ucsc.edu (Ann Zweig)
Date: Mon, 07 Jul 2008 09:06:06 -0700
Subject: [Genome-mirror] hgdownload down?
In-Reply-To: <C3B1193A-6C71-416B-963A-227A3AAAA2C3@ifom-ieo-campus.it>
References: <C3B1193A-6C71-416B-963A-227A3AAAA2C3@ifom-ieo-campus.it>
Message-ID: <48723EEE.7000506@soe.ucsc.edu>

Hello Davide,

	If it was down, it appears to be up now.  Sorry for the 
inconvenience.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


Davide Cittaro wrote:
> Hi all, is hgdownload.cse.ucsc.edu ok? I cannot even ping it... :-(
> 
> Thanks
> 
> d
> 
> 
> /*
> Davide Cittaro
> 
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
> 
> tel.: +39(02)574303007
> e-mail: davide.cittaro at ifom-ieo-campus.it
> */
> 
> 
> 
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror

From hiram at soe.ucsc.edu  Mon Jul  7 09:07:27 2008
From: hiram at soe.ucsc.edu (Hiram Clawson)
Date: Mon, 07 Jul 2008 09:07:27 -0700
Subject: [Genome-mirror] hgdownload down?
In-Reply-To: <C3B1193A-6C71-416B-963A-227A3AAAA2C3@ifom-ieo-campus.it>
References: <C3B1193A-6C71-416B-963A-227A3AAAA2C3@ifom-ieo-campus.it>
Message-ID: <48723F3F.2020608@soe.ucsc.edu>

Good Morning Davide:

The UCSC campus network routing environment had some difficulties
earlier this morning.  The situation has been taken care of and
we should be back to normal.  Our primary WEB site was also
unavailable for a while this morning.

--Hiram

Davide Cittaro wrote:
> Hi all, is hgdownload.cse.ucsc.edu ok? I cannot even ping it... :-(
> 
> Thanks
> 
> d

From weiler at soe.ucsc.edu  Mon Jul  7 09:03:46 2008
From: weiler at soe.ucsc.edu (Erich Weiler)
Date: Mon, 7 Jul 2008 09:03:46 -0700 (PDT)
Subject: [Genome-mirror] hgdownload down?
In-Reply-To: <C3B1193A-6C71-416B-963A-227A3AAAA2C3@ifom-ieo-campus.it>
Message-ID: <262873904.25511215446626701.JavaMail.root@mail-01.cse.ucsc.edu>

Hi-

We had some interesting network issues with our core routers this morning that may have caused some connectivity issues.  It now appears OK for me here - are you still experiencing problems?

-erich

Erich Weiler
CBSE Cluster Admin Group

----- "Davide Cittaro" <davide.cittaro at ifom-ieo-campus.it> wrote:

> Hi all, is hgdownload.cse.ucsc.edu ok? I cannot even ping it... :-(
> 
> Thanks
> 
> d
> 
> 
> /*
> Davide Cittaro
> 
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
> 
> tel.: +39(02)574303007
> e-mail: davide.cittaro at ifom-ieo-campus.it
> */
> 
> 
> 
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror

From davide.cittaro at ifom-ieo-campus.it  Tue Jul  8 01:29:21 2008
From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro)
Date: Tue, 8 Jul 2008 10:29:21 +0200
Subject: [Genome-mirror] hgTracks bug?
Message-ID: <D2BB77C1-14A5-420C-BF6E-1E17DFA5E535@ifom-ieo-campus.it>

Hi all, I've installed v185 and found a weird page layout in hgTracks  
display. I had to modify source of hgTracks.c in this way:

diff -u kent/src/hg/hgTracks/hgTracks.c kent.1/src/hg/hgTracks/ 
hgTracks.c
--- kent/src/hg/hgTracks/hgTracks.c	2008-06-26 20:58:58.000000000 +0200
+++ kent.1/src/hg/hgTracks/hgTracks.c	2008-07-08 10:15:09.000000000  
+0200
@@ -3610,14 +3610,14 @@
              hPrintf("<th align=\"left\" colspan=%d BGCOLOR=#536ED3>",
  	    	    MAX_CONTROL_COLUMNS-1);
  	    }
-	hPrintf("<table width='100%'><tr><td align='left'>");
+	hPrintf("<table width=\"100%%\"><tr><td align='left'>");
  	hPrintf("\n<A NAME=\"%sGroup\"></A>",group->name);
          hPrintf("<A HREF=\"%s?%s&%s=%s#%sGroup\"  
class='bigBlue'><IMG height='18' width='18' onclick=\"return  
toggleTrackGroupVisibility(this, '%s');\" id=\"%s_button\" src=\"%s\"  
alt=\"%s\" class='bigBlue'></A>&nbsp;&nbsp;",
                  hgTracksName(), cartSidUrlString(cart),
                  collapseGroupVar(group->name),
                  otherState, group->name,
                  group->name, group->name, indicatorImg, indicator);
-	hPrintf("</td><td align='center' width='100%'>\n");
+	hPrintf("</td><td align='center' width=\"100%%\">\n");
  	hPrintf("<B>%s</B>", wrapWhiteFont(group->label));
  	hPrintf("</td><td align='right'>\n");
  	hPrintf("<input type='submit' name='submit' value='refresh'>\n");

otherwise blue boxes with track group names won't be displayed  
correctly... i.e. the browser parses misses the '%' character after  
100 in table width and places double quotes somewhere after, so titles  
(such as "Mapping and sequencing tracks") are part of table width as  
long as their HTML tags...
I've noticed your public version doesn't have this issue... I'm  
running here FreeBSD 7 + gcc 4.2.1

Thanks

d


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro at ifom-ieo-campus.it
*/




From davide.cittaro at ifom-ieo-campus.it  Tue Jul  8 01:30:34 2008
From: davide.cittaro at ifom-ieo-campus.it (Davide Cittaro)
Date: Tue, 8 Jul 2008 10:30:34 +0200
Subject: [Genome-mirror] hgdownload down?
In-Reply-To: <48723EEE.7000506@soe.ucsc.edu>
References: <C3B1193A-6C71-416B-963A-227A3AAAA2C3@ifom-ieo-campus.it>
	<48723EEE.7000506@soe.ucsc.edu>
Message-ID: <2BA7DA4B-8550-4389-9CB1-2F4A58829AF8@ifom-ieo-campus.it>

Hello all and thanks for the answer,

On Jul 7, 2008, at 6:06 PM, Ann Zweig wrote:

> Hello Davide,
>
> 	If it was down, it appears to be up now.  Sorry for the  
> inconvenience.
>

It works perfectly, thanks!

d


/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro at ifom-ieo-campus.it
*/




From galt at soe.ucsc.edu  Tue Jul  8 10:22:42 2008
From: galt at soe.ucsc.edu (Galt Barber)
Date: Tue, 8 Jul 2008 10:22:42 -0700 (PDT)
Subject: [Genome-mirror] hgTracks bug?
In-Reply-To: <D2BB77C1-14A5-420C-BF6E-1E17DFA5E535@ifom-ieo-campus.it>
References: <D2BB77C1-14A5-420C-BF6E-1E17DFA5E535@ifom-ieo-campus.it>
Message-ID: <Pine.GSO.4.64.0807081015470.6037@sundance.cse.ucsc.edu>


Hi, Davide!

We added GNU_C var-args syntax checking to hPrintf
just last week and caught this bug and others like
it where programmers forgot to escape the "%"
in the literal to "%%". There were a handful
of others found besides the ones you reported.

The next release should have this fix in it.

Thanks for reporting this.

I think the difference between our system
and yours is that our printf may output a %
even when there is not legal value following it.

But apparently that is platform dependent,
and not guaranteed to work generally anyway
e.g. some legal formatting char like d,u,g,f, etc.
just happens to follow the %, then it will still break.

We have this cleaned up but not on RR yet.
Should be there on v186 next Friday.

-Galt


On Tue, 8 Jul 2008, Davide Cittaro wrote:

> Hi all, I've installed v185 and found a weird page layout in hgTracks
> display. I had to modify source of hgTracks.c in this way:
>
> diff -u kent/src/hg/hgTracks/hgTracks.c kent.1/src/hg/hgTracks/
> hgTracks.c
> --- kent/src/hg/hgTracks/hgTracks.c	2008-06-26 20:58:58.000000000 +0200
> +++ kent.1/src/hg/hgTracks/hgTracks.c	2008-07-08 10:15:09.000000000
> +0200
> @@ -3610,14 +3610,14 @@
>              hPrintf("<th align=\"left\" colspan=%d BGCOLOR=#536ED3>",
>  	    	    MAX_CONTROL_COLUMNS-1);
>  	    }
> -	hPrintf("<table width='100%'><tr><td align='left'>");
> +	hPrintf("<table width=\"100%%\"><tr><td align='left'>");
>  	hPrintf("\n<A NAME=\"%sGroup\"></A>",group->name);
>          hPrintf("<A HREF=\"%s?%s&%s=%s#%sGroup\"
> class='bigBlue'><IMG height='18' width='18' onclick=\"return
> toggleTrackGroupVisibility(this, '%s');\" id=\"%s_button\" src=\"%s\"
> alt=\"%s\" class='bigBlue'></A>&nbsp;&nbsp;",
>                  hgTracksName(), cartSidUrlString(cart),
>                  collapseGroupVar(group->name),
>                  otherState, group->name,
>                  group->name, group->name, indicatorImg, indicator);
> -	hPrintf("</td><td align='center' width='100%'>\n");
> +	hPrintf("</td><td align='center' width=\"100%%\">\n");
>  	hPrintf("<B>%s</B>", wrapWhiteFont(group->label));
>  	hPrintf("</td><td align='right'>\n");
>  	hPrintf("<input type='submit' name='submit' value='refresh'>\n");
>
> otherwise blue boxes with track group names won't be displayed
> correctly... i.e. the browser parses misses the '%' character after
> 100 in table width and places double quotes somewhere after, so titles
> (such as "Mapping and sequencing tracks") are part of table width as
> long as their HTML tags...
> I've noticed your public version doesn't have this issue... I'm
> running here FreeBSD 7 + gcc 4.2.1
>
> Thanks
>
> d
>
>
> /*
> Davide Cittaro
>
> Cogentech - Consortium for Genomic Technologies
> via adamello, 16
> 20139 Milano
> Italy
>
> tel.: +39(02)574303007
> e-mail: davide.cittaro at ifom-ieo-campus.it
> */
>
>
>
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>

From shweta38_sls at students.jnu.ac.in  Sun Jul 13 22:54:10 2008
From: shweta38_sls at students.jnu.ac.in (SHWETA AGGARWAL)
Date: Mon, 14 Jul 2008 11:24:10 +0530
Subject: [Genome-mirror] (no subject)
Message-ID: <487B375A0200006200000106@mail.jnu.ac.in>

HI
I am Shweta, a research scholar in India. I am working on CNV . I am interested in CNV on chromosome 1. I checked for CNV for IL10 and i found  variation in that region according to data published in "Linkage Disequilibrium and Heritability of Copy-NumberPolymorphisms within Duplicated Regions of the Human Genome" by Locke et. al. in 2006. But clone mentioned in database,  RP11-596K11 for CNV on chr 1 actually lies on chromosome 5 according to paper.
Plz let me know what exactly is true.


Thanx
Shweta Aggarwal
Ph.D.
C/O Prof. R.N.K. Bamezai
Cordinator
National Centre of Applied Human Genetics
School of Life Sciences
Jawahwar Lal University
Delhi
India



From rhead at soe.ucsc.edu  Mon Jul 14 12:17:22 2008
From: rhead at soe.ucsc.edu (Brooke Rhead)
Date: Mon, 14 Jul 2008 12:17:22 -0700
Subject: [Genome-mirror] (no subject)
In-Reply-To: <487B375A0200006200000106@mail.jnu.ac.in>
References: <487B375A0200006200000106@mail.jnu.ac.in>
Message-ID: <487BA642.9060806@soe.ucsc.edu>

Hello Shweta,

I cannot speak to the information in the paper you mention, but I can 
tell you how to find more information on the data we present in the 
Genome Browser.  If you click the "mini-button" directly to the left of 
the BAC End Pairs track (the track in which RP11-596K11 appears), or on 
the blue "BAC End Pairs" track name (in the "Mapping and Sequencing 
Tracks" section), you will see details of how that track was created.

The BAC End Pairs track was created by using the BLAT program to align 
BAC clones to the genome sequence.  Chromosome 1 is where the two ends 
of the RP11-596K11 clone aligned.  The authors of the paper in question 
may have used a different method to determine where these BAC ends align 
to the genome.

In the future, please send questions about the Browser to 
genome at soe.ucsc.edu.  This address is specific to users who are running 
mirror sites of the Genome Browser.  More information is here: 
http://genome.ucsc.edu/contacts.html .

--
Brooke Rhead
UCSC Genome Bioinformatics Group


SHWETA AGGARWAL wrote:
> HI
> I am Shweta, a research scholar in India. I am working on CNV . I am interested in CNV on chromosome 1. I checked for CNV for IL10 and i found  variation in that region according to data published in "Linkage Disequilibrium and Heritability of Copy-NumberPolymorphisms within Duplicated Regions of the Human Genome" by Locke et. al. in 2006. But clone mentioned in database,  RP11-596K11 for CNV on chr 1 actually lies on chromosome 5 according to paper.
> Plz let me know what exactly is true.
>
>
> Thanx
> Shweta Aggarwal
> Ph.D.
> C/O Prof. R.N.K. Bamezai
> Cordinator
> National Centre of Applied Human Genetics
> School of Life Sciences
> Jawahwar Lal University
> Delhi
> India
>
>
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>   

From larrym at soe.ucsc.edu  Mon Jul 14 12:00:44 2008
From: larrym at soe.ucsc.edu (Larry Meyer)
Date: Mon, 14 Jul 2008 12:00:44 -0700
Subject: [Genome-mirror] v186 Genome Browser Available
Message-ID: <20080714190044.GD11734@soe.ucsc.edu>

Hello,

The v186 source is now available at:
http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

or labeled with source number:
http://hgdownload.cse.ucsc.edu/admin/jksrc.v186.zip

cartDump cartReset das hgc
hgBlat hgConvert hgCustom hgGateway hgGene hgGenome
hgLiftOver hgNear hgPcr hgSession hgTables hgTracks hgTrackUi
hgVisiGene mkEncodeFrameset hgEncodeDataVersions
pbGateway pbGlobal pbTracks phyloGif

/usr/local/apache/cgi-bin/all.joiner
/usr/local/apache/cgi-bin/galaAvail.tab
/usr/local/apache/cgi-bin/hgNearData/*
/usr/local/apache/cgi-bin/hgGeneData/*
/usr/local/apache/cgi-bin/hgcData/*
/usr/local/apache/cgi-bin/hgCgiData/*
/usr/local/apache/cgi-bin/loader/*
/usr/local/apache/cgi-bin/visiGeneData/*
/usr/local/apache/htdocs/js/*

Contents of v186 may be seen at:

http://genome-test.cse.ucsc.edu/builds/versions.html

Please check both v186-preview and v186-final to see all the code
and data changes in this release.

Larry Meyer
UCSC CBSE

From tedgoldstein at gmail.com  Thu Jul 17 05:08:50 2008
From: tedgoldstein at gmail.com (Ted Goldstein)
Date: Thu, 17 Jul 2008 08:08:50 -0400
Subject: [Genome-mirror] Billions and Billions of Tracks
References: <32b5d5a70807161302v4f489be9le83ee6eb6846f406@mail.gmail.com>
Message-ID: <7A33560B-E38D-4A3F-9EB5-B7ACD1052BAF@gmail.com>

or at least thousands....

I'm visiting Harvard Medical School helping prof Chris Walsh's lab  
this summer for two weeks. Chris' lab is doing gene finding by  
homozygosity mapping of consanguineous (family or cousin) births. They  
have aCGH, SNP and sequence data on about 500 families. With Hiram's  
help, we have succesfully gotten a mirror up and running.  (THANKS  
HIRAM!)

1. I want to make a lab specfic set of categories.  Is the right way  
to do it simply to SQL directly into the local database? e.g.
INSERT INTO grp (name, label, priority) VALUES ("walshLab", "Walsh Lab  
Data", 1.0);

2. They would like random access to their datasets. This means  
something like 500 x N (where N is a number between 2 and 10).
Does it make sense to have a 5000 tracks?

Thanks,
Ted

-- 
Ted Goldstein
1+650.743.4141(mobile)


From fanhsu at soe.ucsc.edu  Thu Jul 17 14:08:24 2008
From: fanhsu at soe.ucsc.edu (Fan Hsu)
Date: Thu, 17 Jul 2008 14:08:24 -0700
Subject: [Genome-mirror] Billions and Billions of Tracks
In-Reply-To: <7A33560B-E38D-4A3F-9EB5-B7ACD1052BAF@gmail.com>
References: <32b5d5a70807161302v4f489be9le83ee6eb6846f406@mail.gmail.com>
	<7A33560B-E38D-4A3F-9EB5-B7ACD1052BAF@gmail.com>
Message-ID: <001201c8e851$40767840$6c00a8c0@duo4t>

Hi Ted,

We had similar experience on dealing with genomic data from more than a
thousand samples for an HIV Vaccine Clinical Trial database we recently
built for a client using UCSC Genome Browser as the base technology.

Assuming that you are not thinking of creating thousands of base genomes,
let's chat if we can share ideas and discuss.

I should be available tomorrow afternoon Pacific time. 

Fan.
-----Original Message-----
From: genome-mirror-bounces at soe.ucsc.edu
[mailto:genome-mirror-bounces at soe.ucsc.edu] On Behalf Of Ted Goldstein
Sent: Thursday, 17 July, 2008 5:09 AM
To: genome-mirror at soe.ucsc.edu
Subject: [Genome-mirror] Billions and Billions of Tracks

or at least thousands....

I'm visiting Harvard Medical School helping prof Chris Walsh's lab  
this summer for two weeks. Chris' lab is doing gene finding by  
homozygosity mapping of consanguineous (family or cousin) births. They  
have aCGH, SNP and sequence data on about 500 families. With Hiram's  
help, we have succesfully gotten a mirror up and running.  (THANKS  
HIRAM!)

1. I want to make a lab specfic set of categories.  Is the right way  
to do it simply to SQL directly into the local database? e.g.
INSERT INTO grp (name, label, priority) VALUES ("walshLab", "Walsh Lab  
Data", 1.0);

2. They would like random access to their datasets. This means  
something like 500 x N (where N is a number between 2 and 10).
Does it make sense to have a 5000 tracks?

Thanks,
Ted

-- 
Ted Goldstein
1+650.743.4141(mobile)

_______________________________________________
Genome-mirror mailing list
Genome-mirror at soe.ucsc.edu
http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror


From hiram at soe.ucsc.edu  Thu Jul 17 14:31:24 2008
From: hiram at soe.ucsc.edu (Hiram Clawson)
Date: Thu, 17 Jul 2008 14:31:24 -0700
Subject: [Genome-mirror] Billions and Billions of Tracks
In-Reply-To: <18559.47264.985894.316585@bugle.cse.ucsc.edu>
References: <32b5d5a70807161302v4f489be9le83ee6eb6846f406@mail.gmail.com>	<7A33560B-E38D-4A3F-9EB5-B7ACD1052BAF@gmail.com>	<61ee49d20807171411g3d0f60e0o8b1f888fd945082a@mail.gmail.com>
	<18559.47264.985894.316585@bugle.cse.ucsc.edu>
Message-ID: <487FBA2C.6000001@soe.ucsc.edu>


Ted:

To add rows to this extra grp_local table, use a simple
insert SQL statement, for example:

INSERT INTO grp_local (name, label, priority, defaultIsClosed)
VALUES ('map','Mapping and Sequencing Tracks',2,0);

To create the table:

CREATE TABLE grp_local (
   name char(255) NOT NULL default '',
   label char(255) NOT NULL default '',
   priority float NOT NULL default '0',
   defaultIsClosed int(11) default NULL,
   PRIMARY KEY  (name)
) TYPE=MyISAM;

--Hiram

Mark Diekhans wrote:
> There is actually a facility for having multiple trackDb and grp
> tables that are merging at run time, functioning much like a Unix
> PATH (first definition of a table is used).  I hasn't been documented,
> however I just added a brief description of how to set it up in:
> 
>         kent/src/product/ex.hg.conf
> 
> mark
> 
> Michael Pheasant <mike at pheasant.co.nz> writes:
>> Hi
>>
>> We had a similar problem in AU with needing to create groups of tracks for
>> different users.
>> Mirror sites cannot update any of the tables (or any other files) that are
>> updated by the rsync process, which means things like grp tables and .ra
>> files are out-of-bounds.
>>
>> I ended up rsyncing tables like grp to a different local name and created
>> views which make the union of the rsync'd table and the local table. Gets
>> quite complicated.
>>
>> *) Is there a recommended solution for this sort of problem for mirrors?
>>
>> Mike
>>
>> On Thu, Jul 17, 2008 at 5:08 AM, Ted Goldstein <tedgoldstein at gmail.com>
>> wrote:
>>
>>> or at least thousands....
>>>
>>> I'm visiting Harvard Medical School helping prof Chris Walsh's lab
>>> this summer for two weeks. Chris' lab is doing gene finding by
>>> homozygosity mapping of consanguineous (family or cousin) births. They
>>> have aCGH, SNP and sequence data on about 500 families. With Hiram's
>>> help, we have succesfully gotten a mirror up and running.  (THANKS
>>> HIRAM!)
>>>
>>> 1. I want to make a lab specfic set of categories.  Is the right way
>>> to do it simply to SQL directly into the local database? e.g.
>>> INSERT INTO grp (name, label, priority) VALUES ("walshLab", "Walsh Lab
>>> Data", 1.0);
>>>
>>> 2. They would like random access to their datasets. This means
>>> something like 500 x N (where N is a number between 2 and 10).
>>> Does it make sense to have a 5000 tracks?
>>>
>>> Thanks,
>>> Ted
>>>
>>> --
>>> Ted Goldstein
>>> 1+650.743.4141(mobile)
>>>
>>> _______________________________________________
>>> Genome-mirror mailing list
>>> Genome-mirror at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>>>
>>
>>
>> -- 
>> Michael Pheasant
>> Associate Project Scientist
>> UCSC Genome Browser
>>
>> Email: mikep at soe.ucsc.edu
>> Skype: mpheasant at skype.com
>> Phone: +1-831-706-2689
>> ll=36.953713,-122.033153
>>
>> Location: Engineering2 Room 515
>> Post: CBSE, UC Santa Cruz, MS:CBSE/ITI
>> 1156 High Street
>> Santa Cruz, CA 95064, USA
> 

From markd at soe.ucsc.edu  Thu Jul 17 14:24:48 2008
From: markd at soe.ucsc.edu (Mark Diekhans)
Date: Thu, 17 Jul 2008 14:24:48 -0700
Subject: [Genome-mirror] Billions and Billions of Tracks
In-Reply-To: <61ee49d20807171411g3d0f60e0o8b1f888fd945082a@mail.gmail.com>
References: <32b5d5a70807161302v4f489be9le83ee6eb6846f406@mail.gmail.com>
	<7A33560B-E38D-4A3F-9EB5-B7ACD1052BAF@gmail.com>
	<61ee49d20807171411g3d0f60e0o8b1f888fd945082a@mail.gmail.com>
Message-ID: <18559.47264.985894.316585@bugle.cse.ucsc.edu>


There is actually a facility for having multiple trackDb and grp
tables that are merging at run time, functioning much like a Unix
PATH (first definition of a table is used).  I hasn't been documented,
however I just added a brief description of how to set it up in:

        kent/src/product/ex.hg.conf

mark

Michael Pheasant <mike at pheasant.co.nz> writes:
> Hi
> 
> We had a similar problem in AU with needing to create groups of tracks for
> different users.
> Mirror sites cannot update any of the tables (or any other files) that are
> updated by the rsync process, which means things like grp tables and .ra
> files are out-of-bounds.
> 
> I ended up rsyncing tables like grp to a different local name and created
> views which make the union of the rsync'd table and the local table. Gets
> quite complicated.
> 
> *) Is there a recommended solution for this sort of problem for mirrors?
> 
> Mike
> 
> On Thu, Jul 17, 2008 at 5:08 AM, Ted Goldstein <tedgoldstein at gmail.com>
> wrote:
> 
> > or at least thousands....
> >
> > I'm visiting Harvard Medical School helping prof Chris Walsh's lab
> > this summer for two weeks. Chris' lab is doing gene finding by
> > homozygosity mapping of consanguineous (family or cousin) births. They
> > have aCGH, SNP and sequence data on about 500 families. With Hiram's
> > help, we have succesfully gotten a mirror up and running.  (THANKS
> > HIRAM!)
> >
> > 1. I want to make a lab specfic set of categories.  Is the right way
> > to do it simply to SQL directly into the local database? e.g.
> > INSERT INTO grp (name, label, priority) VALUES ("walshLab", "Walsh Lab
> > Data", 1.0);
> >
> > 2. They would like random access to their datasets. This means
> > something like 500 x N (where N is a number between 2 and 10).
> > Does it make sense to have a 5000 tracks?
> >
> > Thanks,
> > Ted
> >
> > --
> > Ted Goldstein
> > 1+650.743.4141(mobile)
> >
> > _______________________________________________
> > Genome-mirror mailing list
> > Genome-mirror at soe.ucsc.edu
> > http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
> >
> 
> 
> 
> -- 
> Michael Pheasant
> Associate Project Scientist
> UCSC Genome Browser
> 
> Email: mikep at soe.ucsc.edu
> Skype: mpheasant at skype.com
> Phone: +1-831-706-2689
> ll=36.953713,-122.033153
> 
> Location: Engineering2 Room 515
> Post: CBSE, UC Santa Cruz, MS:CBSE/ITI
> 1156 High Street
> Santa Cruz, CA 95064, USA

From Janet_Yang at dfci.harvard.edu  Mon Jul 21 10:53:07 2008
From: Janet_Yang at dfci.harvard.edu (Yang, Janet Q.)
Date: Mon, 21 Jul 2008 13:53:07 -0400
Subject: [Genome-mirror] Access  isPCR(UCSC) from command line interface
Message-ID: <E53BDDA9FB1D3D429048369D6C6E258408A035@PHSXMB4.partners.org>

Hi UCSC Staff,

 

I  have down loaded whole UCSC Genome Browser to our server. I only run it from
website.  Is there any way I can start UCSC Genome Browser via  command line on
my server?  Especially  start  " In Silico PCR"  on my server (use what
command)?  

 

Thank you very much for your help!

 

Sincerely,

 

Janet Yang

DANA-FARBER CANCER INSTITUTE


The information transmitted in this electronic communication is intended only
for the person or entity to whom it is addressed and may contain confidential
and/or privileged material. Any review, retransmission, dissemination or other
use of or taking of any action in reliance upon this information by persons or
entities other than the intended recipient is prohibited. If you received this
information in error, please contact the Compliance HelpLine at 800-856-1983 and
properly dispose of this information.



From rhead at soe.ucsc.edu  Mon Jul 21 19:15:06 2008
From: rhead at soe.ucsc.edu (Brooke Rhead)
Date: Mon, 21 Jul 2008 19:15:06 -0700
Subject: [Genome-mirror] Access isPCR(UCSC) from command line interface
In-Reply-To: <E53BDDA9FB1D3D429048369D6C6E258408A035@PHSXMB4.partners.org>
References: <E53BDDA9FB1D3D429048369D6C6E258408A035@PHSXMB4.partners.org>
Message-ID: <488542AA.3040806@soe.ucsc.edu>

Hello Janet,

If you have downloaded the Genome Browser source code and followed the 
build instructions:
http://genome.ucsc.edu/admin/jk-install.html

you can use the command "isPcr" to run isPCR at the command line.  If 
you run it with no arguments, you will get a usage statement:


$ isPcr
isPcr - Standalone v 34x2 In-Situ PCR Program
usage:
   isPcr database query output
where database is a fasta, nib, or twoBit file or a text file containing
a list of these files,  query is a text file file containing three 
columns: name,
forward primer, and reverse primer,  and output is where the results go.
The names 'stdin' and 'stdout' can be used as file names to make using the
program in pipes easier.
options:
   -ooc=N.ooc  Use overused tile file N.ooc.  N should correspond to
               the tileSize
   -tileSize=N the size of match that triggers an alignment. 
               Default is 11 .
   -stepSize=N spacing between tiles. Default is 5.
   -maxSize=N - Maximum size of PCR product (default 4000)
   -minSize=N - Minimum size of PCR product (default 0)
   -minPerfect=N - Minimum size of perfect match at 3' end of primer 
(default 15)
   -minGood=N - Minimum size where there must be 2 matches for each 
mismatch (default 15)
   -mask=type  Mask out repeats.  Alignments won't be started in masked 
region
               but may extend through it in nucleotide searches.  Masked 
areas
               are ignored entirely in protein or translated searches. 
Types are
                 lower - mask out lower cased sequence
                 upper - mask out upper cased sequence
                 out   - mask according to database.out RepeatMasker 
.out file
                 file.out - mask database according to RepeatMasker file.out
   -makeOoc=N.ooc Make overused tile file. Database needs to be complete 
genome.
   -repMatch=N sets the number of repetitions of a tile allowed before
               it is marked as overused.  Typically this is 256 for tileSize
               12, 1024 for tile size 11, 4096 for tile size 10.
               Default is 1024.  Only comes into play with makeOoc
   -flipReverse Reverse complement reverse (second) primer before using
   -out=XXX - Output format.  Either
      fa - fasta with position, primers in header (default)
      bed - tab delimited format. Fields: chrom/start/end/name/score/strand
      psl - blat format.

I hope this is helpful.  Please feel free to email the mail list again 
if you have further questions.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Yang, Janet Q. wrote:
> Hi UCSC Staff,
>
>  
>
> I  have down loaded whole UCSC Genome Browser to our server. I only run it from
> website.  Is there any way I can start UCSC Genome Browser via  command line on
> my server?  Especially  start  " In Silico PCR"  on my server (use what
> command)?  
>
>  
>
> Thank you very much for your help!
>
>  
>
> Sincerely,
>
>  
>
> Janet Yang
>
> DANA-FARBER CANCER INSTITUTE
>
>
> The information transmitted in this electronic communication is intended only
> for the person or entity to whom it is addressed and may contain confidential
> and/or privileged material. Any review, retransmission, dissemination or other
> use of or taking of any action in reliance upon this information by persons or
> entities other than the intended recipient is prohibited. If you received this
> information in error, please contact the Compliance HelpLine at 800-856-1983 and
> properly dispose of this information.
>
>
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>   

From kayla at soe.ucsc.edu  Tue Jul 22 11:51:37 2008
From: kayla at soe.ucsc.edu (Kayla Smith)
Date: Tue, 22 Jul 2008 11:51:37 -0700
Subject: [Genome-mirror] release of new assembly: ce6
Message-ID: <48862C39.1030504@cse.ucsc.edu>

Hello Mirror sites,

We are planning to release a new browser for C. elegans, ce6, soon.
   Please be prepared to host the following data:

ce6 mySQL tables:  3 GB
/gbdb/ce6/* files:  856 MB

We will also be releasing net and chain tracks to ce6 in the following
assembly databases.  Here are the approximate sizes of the netCe6 and
%chainCe6% tables in each database:

priPac1: 21 MB
caePb2: 138 MB
caeRem3:137 MB
cb3:    174 MB
caeJap1: 78 MB
_______
total: ~548 MB

Please let us know if you have any questions or concerns:

Kayla Smith
UCSC Genome Bioinformatics Group

From Janet_Yang at dfci.harvard.edu  Wed Jul 23 13:03:11 2008
From: Janet_Yang at dfci.harvard.edu (Yang, Janet Q.)
Date: Wed, 23 Jul 2008 16:03:11 -0400
Subject: [Genome-mirror] About session settings
Message-ID: <E53BDDA9FB1D3D429048369D6C6E258408A043@PHSXMB4.partners.org>

Hi UCSC Staff,

 

I have down loaded whole UCSC Genome Browser binary code to our server. Now we
can run Genome Browser locally.

When Dr. Miron (my boss) ran the Genome Browser "Session" part (from In Silico
PCR <http://miron.dfci.harvard.edu/cgi-bin/hgPcr>  to Session) each time, He
found that his previous Session setting was always changed.

 

We thought "Session" is on our server, and only Dr. Miron uses it.  Is the
"session" linked to somewhere,  people all  use it?

 

Is there any way the "Session "setting can be saved in our local server or some
where, so next time he can reenter and continue his work? 

 

Thank you very much for your time and help!

 

Sincerely,

 

Janet

 


The information transmitted in this electronic communication is intended only
for the person or entity to whom it is addressed and may contain confidential
and/or privileged material. Any review, retransmission, dissemination or other
use of or taking of any action in reliance upon this information by persons or
entities other than the intended recipient is prohibited. If you received this
information in error, please contact the Compliance HelpLine at 800-856-1983 and
properly dispose of this information.



From pauline at soe.ucsc.edu  Wed Jul 23 16:53:08 2008
From: pauline at soe.ucsc.edu (Pauline Fujita)
Date: Wed, 23 Jul 2008 16:53:08 -0700
Subject: [Genome-mirror] About session settings
In-Reply-To: <E53BDDA9FB1D3D429048369D6C6E258408A043@PHSXMB4.partners.org>
References: <E53BDDA9FB1D3D429048369D6C6E258408A043@PHSXMB4.partners.org>
Message-ID: <4887C464.3010308@soe.ucsc.edu>

Hello Janet,

You may find this thread on session set up useful:

https://www.soe.ucsc.edu/pipermail/genome-mirror/2007-February/thread.html#345 


Also, if you want to read more about cookies you can find a brief 
description here:

http://genomewiki.ucsc.edu/index.php/Cookie_Session

and a more detailed discussion in this mailing list thread:

https://www.soe.ucsc.edu/pipermail/genome-mirror/2007-November/000657.html

Hopefully this information is enough to get you started. If you have 
further questions please continue sending them to the genome-mirror 
mailing list at genome-mirror at soe.ucsc.edu.

Regards,

Pauline Fujita

UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Yang, Janet Q. wrote:
> Hi UCSC Staff,
>
>  
>
> I have down loaded whole UCSC Genome Browser binary code to our server. Now we
> can run Genome Browser locally.
>
> When Dr. Miron (my boss) ran the Genome Browser "Session" part (from In Silico
> PCR <http://miron.dfci.harvard.edu/cgi-bin/hgPcr>  to Session) each time, He
> found that his previous Session setting was always changed.
>
>  
>
> We thought "Session" is on our server, and only Dr. Miron uses it.  Is the
> "session" linked to somewhere,  people all  use it?
>
>  
>
> Is there any way the "Session "setting can be saved in our local server or some
> where, so next time he can reenter and continue his work? 
>
>  
>
> Thank you very much for your time and help!
>
>  
>
> Sincerely,
>
>  
>
> Janet
>
>  
>
>
> The information transmitted in this electronic communication is intended only
> for the person or entity to whom it is addressed and may contain confidential
> and/or privileged material. Any review, retransmission, dissemination or other
> use of or taking of any action in reliance upon this information by persons or
> entities other than the intended recipient is prohibited. If you received this
> information in error, please contact the Compliance HelpLine at 800-856-1983 and
> properly dispose of this information.
>
>
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>   


From rhead at soe.ucsc.edu  Wed Jul 23 17:29:16 2008
From: rhead at soe.ucsc.edu (Brooke Rhead)
Date: Wed, 23 Jul 2008 17:29:16 -0700
Subject: [Genome-mirror] expect 16GB of new data in /gbdb/hg18/snp
Message-ID: <4887CCDC.5050603@soe.ucsc.edu>

Hello Mirror Sites,

We will be adding a 16GB file to the /gbdb area early next week.  It 
consists of a single file:

/gbdb/hg18/snp/snp129.fa

This is in preparation for the dbSNP build 129 SNPs track.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

From dereje1227 at yahoo.com  Thu Jul 24 06:58:01 2008
From: dereje1227 at yahoo.com (Dereje Demissie)
Date: Thu, 24 Jul 2008 06:58:01 -0700 (PDT)
Subject: [Genome-mirror] downlaoding UCSC ncRNA annotations
Message-ID: <806751.28103.qm@web56902.mail.re3.yahoo.com>

Would you please guide me how should I download USC ncRNA annotations as a table format? I know the hard way using script and parsing to my local database. I thought there might be an easy way. I can't able to find in human annotation ?download list.
?
With Best regards
Dereje
?


      

From wuko at mail.nih.gov  Fri Jul 25 07:00:16 2008
From: wuko at mail.nih.gov (Wu, Kotien (NIH/NCI) [E])
Date: Fri, 25 Jul 2008 10:00:16 -0400
Subject: [Genome-mirror] make installation in kent/src/hg/js
Message-ID: <D54AB1BFDE02B9449144D34E6F58499C02CC371C@nihcesmlbx10.nih.gov>

Our machine is x86_64 GNU/Linux. 

 

When we do installation in kent/src/hg/js

 

run 

 

doInstall:

        @mkdir -p ${DEST}/

        rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
${DEST}/

 

in the makefile over there.

 

we got

 

make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'

rsync -t -r --relative --exclude='makefile'  `cvsFiles`
/usr/local/apache/htdocs/js/

/bin/sh: cvsFiles: command not found

rsync  version 2.6.3  protocol version 28

Copyright (C) 1996-2004 by Andrew Tridgell and others

<http://rsync.samba.org/>

 

......

 

Please see the rsync(1) and rsyncd.conf(5) man pages for full
documentation

See http://rsync.samba.org/ for updates, bug reports, and answers

rsync error: syntax or usage error (code 1) at main.c(891)

make[2]: *** [doInstall] Error 1

 

If I comment out ${EXCL} `cvsFiles` and run as

 

doInstall:

        @mkdir -p ${DEST}/

        rsync -t -r --relative --exclude='makefile' ${DEST}/

        ## rsync -t -r --relative --exclude='makefile' ${EXCL}
`cvsFiles` ${DEST}/

 

We got similar error message without '/bin/sh: cvsFiles: command not
found'.

 

Could you please help us, what we need to do?

 

Thanks a lot!

 

Kotien

 


From ann at soe.ucsc.edu  Fri Jul 25 09:32:43 2008
From: ann at soe.ucsc.edu (Ann Zweig)
Date: Fri, 25 Jul 2008 09:32:43 -0700
Subject: [Genome-mirror] make installation in kent/src/hg/js
In-Reply-To: <D54AB1BFDE02B9449144D34E6F58499C02CC371C@nihcesmlbx10.nih.gov>
References: <D54AB1BFDE02B9449144D34E6F58499C02CC371C@nihcesmlbx10.nih.gov>
Message-ID: <488A002B.8080700@soe.ucsc.edu>

Hello Kotien,

	It appears that this new step hasn't been added to our mirror procedures help 
page yet: http://genome.ucsc.edu/admin/mirror.html

	I will explain here what you need to to.

The cvsFiles lives here:  kent/src/utils/cvsTools/cvsFiles

It is installed when one runs 'make scripts' or 'make alpha' in
kent/src/utils/.  Unfortunately kent/src/makefile invokes plain old 'make'
in utils -- for 'make', but not for 'make alpha', in kent/src.  Bottom
line is, a top-level build does not install cvsFiles in BINDIR but it
should.	



Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Wu, Kotien (NIH/NCI) [E] wrote:
> Our machine is x86_64 GNU/Linux. 
> 
>  
> 
> When we do installation in kent/src/hg/js
> 
>  
> 
> run 
> 
>  
> 
> doInstall:
> 
>         @mkdir -p ${DEST}/
> 
>         rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
> ${DEST}/
> 
>  
> 
> in the makefile over there.
> 
>  
> 
> we got
> 
>  
> 
> make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'
> 
> rsync -t -r --relative --exclude='makefile'  `cvsFiles`
> /usr/local/apache/htdocs/js/
> 
> /bin/sh: cvsFiles: command not found
> 
> rsync  version 2.6.3  protocol version 28
> 
> Copyright (C) 1996-2004 by Andrew Tridgell and others
> 
> <http://rsync.samba.org/>
> 
>  
> 
> ......
> 
>  
> 
> Please see the rsync(1) and rsyncd.conf(5) man pages for full
> documentation
> 
> See http://rsync.samba.org/ for updates, bug reports, and answers
> 
> rsync error: syntax or usage error (code 1) at main.c(891)
> 
> make[2]: *** [doInstall] Error 1
> 
>  
> 
> If I comment out ${EXCL} `cvsFiles` and run as
> 
>  
> 
> doInstall:
> 
>         @mkdir -p ${DEST}/
> 
>         rsync -t -r --relative --exclude='makefile' ${DEST}/
> 
>         ## rsync -t -r --relative --exclude='makefile' ${EXCL}
> `cvsFiles` ${DEST}/
> 
>  
> 
> We got similar error message without '/bin/sh: cvsFiles: command not
> found'.
> 
>  
> 
> Could you please help us, what we need to do?
> 
>  
> 
> Thanks a lot!
> 
>  
> 
> Kotien
> 
>  
> 
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror

From wuko at mail.nih.gov  Fri Jul 25 09:54:09 2008
From: wuko at mail.nih.gov (Wu, Kotien (NIH/NCI) [E])
Date: Fri, 25 Jul 2008 12:54:09 -0400
Subject: [Genome-mirror] make installation in kent/src/hg/js
In-Reply-To: <488A002B.8080700@soe.ucsc.edu>
Message-ID: <D54AB1BFDE02B9449144D34E6F58499C02CC3720@nihcesmlbx10.nih.gov>

It looks that I hit the new problem:

bash-3.00# pwd
/app1/data10/intel/jksrc/kent/src/utils
bash-3.00# make scripts
cp -p agpToLift /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
cp -p iSync /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
cp -p lodToBedScore /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
cp -p mkMafFrames.pl /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
make: *** [scripts] Error 1

or

bash-3.00# make alpha
cp -p agpToLift /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
cp -p iSync /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
cp -p lodToBedScore /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
cp -p mkMafFrames.pl /cluster/bin/scripts
cp: cannot create regular file `/cluster/bin/scripts': No such file or
directory
make: *** [scripts] Error 1


In our root, we don't have dir cluster/bin.

Do I need to create dir cluster/bin at root dir?

Also how about error message:
rsync error: syntax or usage error (code 1) at main.c(891)

which came out even I comment out cvsFiles stuff.

Many thanks!

Kotien

-----Original Message-----
From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
Sent: Friday, July 25, 2008 12:33 PM
To: Wu, Kotien (NIH/NCI) [E]
Cc: genome-mirror at cse.ucsc.edu
Subject: Re: [Genome-mirror] make installation in kent/src/hg/js

Hello Kotien,

	It appears that this new step hasn't been added to our mirror
procedures help 
page yet: http://genome.ucsc.edu/admin/mirror.html

	I will explain here what you need to to.

The cvsFiles lives here:  kent/src/utils/cvsTools/cvsFiles

It is installed when one runs 'make scripts' or 'make alpha' in
kent/src/utils/.  Unfortunately kent/src/makefile invokes plain old
'make'
in utils -- for 'make', but not for 'make alpha', in kent/src.  Bottom
line is, a top-level build does not install cvsFiles in BINDIR but it
should.	



Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Wu, Kotien (NIH/NCI) [E] wrote:
> Our machine is x86_64 GNU/Linux. 
> 
>  
> 
> When we do installation in kent/src/hg/js
> 
>  
> 
> run 
> 
>  
> 
> doInstall:
> 
>         @mkdir -p ${DEST}/
> 
>         rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
> ${DEST}/
> 
>  
> 
> in the makefile over there.
> 
>  
> 
> we got
> 
>  
> 
> make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'
> 
> rsync -t -r --relative --exclude='makefile'  `cvsFiles`
> /usr/local/apache/htdocs/js/
> 
> /bin/sh: cvsFiles: command not found
> 
> rsync  version 2.6.3  protocol version 28
> 
> Copyright (C) 1996-2004 by Andrew Tridgell and others
> 
> <http://rsync.samba.org/>
> 
>  
> 
> ......
> 
>  
> 
> Please see the rsync(1) and rsyncd.conf(5) man pages for full
> documentation
> 
> See http://rsync.samba.org/ for updates, bug reports, and answers
> 
> rsync error: syntax or usage error (code 1) at main.c(891)
> 
> make[2]: *** [doInstall] Error 1
> 
>  
> 
> If I comment out ${EXCL} `cvsFiles` and run as
> 
>  
> 
> doInstall:
> 
>         @mkdir -p ${DEST}/
> 
>         rsync -t -r --relative --exclude='makefile' ${DEST}/
> 
>         ## rsync -t -r --relative --exclude='makefile' ${EXCL}
> `cvsFiles` ${DEST}/
> 
>  
> 
> We got similar error message without '/bin/sh: cvsFiles: command not
> found'.
> 
>  
> 
> Could you please help us, what we need to do?
> 
>  
> 
> Thanks a lot!
> 
>  
> 
> Kotien
> 
>  
> 
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror


From ann at soe.ucsc.edu  Fri Jul 25 11:33:12 2008
From: ann at soe.ucsc.edu (Ann Zweig)
Date: Fri, 25 Jul 2008 11:33:12 -0700
Subject: [Genome-mirror] make installation in kent/src/hg/js
In-Reply-To: <D54AB1BFDE02B9449144D34E6F58499C02CC3720@nihcesmlbx10.nih.gov>
References: <D54AB1BFDE02B9449144D34E6F58499C02CC3720@nihcesmlbx10.nih.gov>
Message-ID: <488A1C68.6000407@soe.ucsc.edu>

Hello again, Kotien,

The makefile in kent/src/utils uses the SCRIPTS make variable.  You will need to 
override that like so:

	cd kent/src/scripts
	make SCRIPTS=/a/directory/here alpha

You should use a directory that's already in your path environment variable, 
e.g. /usr/local/bin.

	We are still looking into the rsync error.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu





Wu, Kotien (NIH/NCI) [E] wrote:
> It looks that I hit the new problem:
> 
> bash-3.00# pwd
> /app1/data10/intel/jksrc/kent/src/utils
> bash-3.00# make scripts
> cp -p agpToLift /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> cp -p iSync /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> cp -p lodToBedScore /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> cp -p mkMafFrames.pl /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> make: *** [scripts] Error 1
> 
> or
> 
> bash-3.00# make alpha
> cp -p agpToLift /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> cp -p iSync /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> cp -p lodToBedScore /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> cp -p mkMafFrames.pl /cluster/bin/scripts
> cp: cannot create regular file `/cluster/bin/scripts': No such file or
> directory
> make: *** [scripts] Error 1
> 
> 
> In our root, we don't have dir cluster/bin.
> 
> Do I need to create dir cluster/bin at root dir?
> 
> Also how about error message:
> rsync error: syntax or usage error (code 1) at main.c(891)
> 
> which came out even I comment out cvsFiles stuff.
> 
> Many thanks!
> 
> Kotien
> 
> -----Original Message-----
> From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
> Sent: Friday, July 25, 2008 12:33 PM
> To: Wu, Kotien (NIH/NCI) [E]
> Cc: genome-mirror at cse.ucsc.edu
> Subject: Re: [Genome-mirror] make installation in kent/src/hg/js
> 
> Hello Kotien,
> 
> 	It appears that this new step hasn't been added to our mirror
> procedures help 
> page yet: http://genome.ucsc.edu/admin/mirror.html
> 
> 	I will explain here what you need to to.
> 
> The cvsFiles lives here:  kent/src/utils/cvsTools/cvsFiles
> 
> It is installed when one runs 'make scripts' or 'make alpha' in
> kent/src/utils/.  Unfortunately kent/src/makefile invokes plain old
> 'make'
> in utils -- for 'make', but not for 'make alpha', in kent/src.  Bottom
> line is, a top-level build does not install cvsFiles in BINDIR but it
> should.	
> 
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> 
> Wu, Kotien (NIH/NCI) [E] wrote:
>> Our machine is x86_64 GNU/Linux. 
>>
>>  
>>
>> When we do installation in kent/src/hg/js
>>
>>  
>>
>> run 
>>
>>  
>>
>> doInstall:
>>
>>         @mkdir -p ${DEST}/
>>
>>         rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
>> ${DEST}/
>>
>>  
>>
>> in the makefile over there.
>>
>>  
>>
>> we got
>>
>>  
>>
>> make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'
>>
>> rsync -t -r --relative --exclude='makefile'  `cvsFiles`
>> /usr/local/apache/htdocs/js/
>>
>> /bin/sh: cvsFiles: command not found
>>
>> rsync  version 2.6.3  protocol version 28
>>
>> Copyright (C) 1996-2004 by Andrew Tridgell and others
>>
>> <http://rsync.samba.org/>
>>
>>  
>>
>> ......
>>
>>  
>>
>> Please see the rsync(1) and rsyncd.conf(5) man pages for full
>> documentation
>>
>> See http://rsync.samba.org/ for updates, bug reports, and answers
>>
>> rsync error: syntax or usage error (code 1) at main.c(891)
>>
>> make[2]: *** [doInstall] Error 1
>>
>>  
>>
>> If I comment out ${EXCL} `cvsFiles` and run as
>>
>>  
>>
>> doInstall:
>>
>>         @mkdir -p ${DEST}/
>>
>>         rsync -t -r --relative --exclude='makefile' ${DEST}/
>>
>>         ## rsync -t -r --relative --exclude='makefile' ${EXCL}
>> `cvsFiles` ${DEST}/
>>
>>  
>>
>> We got similar error message without '/bin/sh: cvsFiles: command not
>> found'.
>>
>>  
>>
>> Could you please help us, what we need to do?
>>
>>  
>>
>> Thanks a lot!
>>
>>  
>>
>> Kotien
>>
>>  
>>
>> _______________________________________________
>> Genome-mirror mailing list
>> Genome-mirror at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror

From ann at soe.ucsc.edu  Fri Jul 25 12:40:02 2008
From: ann at soe.ucsc.edu (Ann Zweig)
Date: Fri, 25 Jul 2008 12:40:02 -0700
Subject: [Genome-mirror] make installation in kent/src/hg/js
In-Reply-To: <488A1C68.6000407@soe.ucsc.edu>
References: <D54AB1BFDE02B9449144D34E6F58499C02CC3720@nihcesmlbx10.nih.gov>
	<488A1C68.6000407@soe.ucsc.edu>
Message-ID: <488A2C12.1080503@soe.ucsc.edu>

Hi Kotien,

	A developer here proposes that the rsync error isn't really an error.  If you 
'man rsync', you'll see it requires a SRC and DEST argument.  You removed
the SRC part of the rsync arguments, hence the rsync error.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Ann Zweig wrote:
> Hello again, Kotien,
> 
> The makefile in kent/src/utils uses the SCRIPTS make variable.  You will need to 
> override that like so:
> 
> 	cd kent/src/scripts
> 	make SCRIPTS=/a/directory/here alpha
> 
> You should use a directory that's already in your path environment variable, 
> e.g. /usr/local/bin.
> 
> 	We are still looking into the rsync error.
> 
> 
> Regards,
> 
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
> 
> 
> 
> 
> 
> Wu, Kotien (NIH/NCI) [E] wrote:
>> It looks that I hit the new problem:
>>
>> bash-3.00# pwd
>> /app1/data10/intel/jksrc/kent/src/utils
>> bash-3.00# make scripts
>> cp -p agpToLift /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p iSync /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p lodToBedScore /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p mkMafFrames.pl /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> make: *** [scripts] Error 1
>>
>> or
>>
>> bash-3.00# make alpha
>> cp -p agpToLift /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p iSync /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p lodToBedScore /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p mkMafFrames.pl /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> make: *** [scripts] Error 1
>>
>>
>> In our root, we don't have dir cluster/bin.
>>
>> Do I need to create dir cluster/bin at root dir?
>>
>> Also how about error message:
>> rsync error: syntax or usage error (code 1) at main.c(891)
>>
>> which came out even I comment out cvsFiles stuff.
>>
>> Many thanks!
>>
>> Kotien
>>
>> -----Original Message-----
>> From: Ann Zweig [mailto:ann at soe.ucsc.edu] 
>> Sent: Friday, July 25, 2008 12:33 PM
>> To: Wu, Kotien (NIH/NCI) [E]
>> Cc: genome-mirror at cse.ucsc.edu
>> Subject: Re: [Genome-mirror] make installation in kent/src/hg/js
>>
>> Hello Kotien,
>>
>> 	It appears that this new step hasn't been added to our mirror
>> procedures help 
>> page yet: http://genome.ucsc.edu/admin/mirror.html
>>
>> 	I will explain here what you need to to.
>>
>> The cvsFiles lives here:  kent/src/utils/cvsTools/cvsFiles
>>
>> It is installed when one runs 'make scripts' or 'make alpha' in
>> kent/src/utils/.  Unfortunately kent/src/makefile invokes plain old
>> 'make'
>> in utils -- for 'make', but not for 'make alpha', in kent/src.  Bottom
>> line is, a top-level build does not install cvsFiles in BINDIR but it
>> should.	
>>
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>>
>> Wu, Kotien (NIH/NCI) [E] wrote:
>>> Our machine is x86_64 GNU/Linux. 
>>>
>>>  
>>>
>>> When we do installation in kent/src/hg/js
>>>
>>>  
>>>
>>> run 
>>>
>>>  
>>>
>>> doInstall:
>>>
>>>         @mkdir -p ${DEST}/
>>>
>>>         rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
>>> ${DEST}/
>>>
>>>  
>>>
>>> in the makefile over there.
>>>
>>>  
>>>
>>> we got
>>>
>>>  
>>>
>>> make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'
>>>
>>> rsync -t -r --relative --exclude='makefile'  `cvsFiles`
>>> /usr/local/apache/htdocs/js/
>>>
>>> /bin/sh: cvsFiles: command not found
>>>
>>> rsync  version 2.6.3  protocol version 28
>>>
>>> Copyright (C) 1996-2004 by Andrew Tridgell and others
>>>
>>> <http://rsync.samba.org/>
>>>
>>>  
>>>
>>> ......
>>>
>>>  
>>>
>>> Please see the rsync(1) and rsyncd.conf(5) man pages for full
>>> documentation
>>>
>>> See http://rsync.samba.org/ for updates, bug reports, and answers
>>>
>>> rsync error: syntax or usage error (code 1) at main.c(891)
>>>
>>> make[2]: *** [doInstall] Error 1
>>>
>>>  
>>>
>>> If I comment out ${EXCL} `cvsFiles` and run as
>>>
>>>  
>>>
>>> doInstall:
>>>
>>>         @mkdir -p ${DEST}/
>>>
>>>         rsync -t -r --relative --exclude='makefile' ${DEST}/
>>>
>>>         ## rsync -t -r --relative --exclude='makefile' ${EXCL}
>>> `cvsFiles` ${DEST}/
>>>
>>>  
>>>
>>> We got similar error message without '/bin/sh: cvsFiles: command not
>>> found'.
>>>
>>>  
>>>
>>> Could you please help us, what we need to do?
>>>
>>>  
>>>
>>> Thanks a lot!
>>>
>>>  
>>>
>>> Kotien
>>>
>>>  
>>>
>>> _______________________________________________
>>> Genome-mirror mailing list
>>> Genome-mirror at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror

From mikep at soe.ucsc.edu  Fri Jul 25 13:10:34 2008
From: mikep at soe.ucsc.edu (Michael Pheasant)
Date: Fri, 25 Jul 2008 13:10:34 -0700
Subject: [Genome-mirror] make installation in kent/src/hg/js
In-Reply-To: <488A2C12.1080503@soe.ucsc.edu>
References: <D54AB1BFDE02B9449144D34E6F58499C02CC3720@nihcesmlbx10.nih.gov>
	<488A1C68.6000407@soe.ucsc.edu> <488A2C12.1080503@soe.ucsc.edu>
Message-ID: <61ee49d20807251310p5c98fcfbo2dc9d0d1946a34a7@mail.gmail.com>

Hi Kotien

Are you making a mirror using a CVS version of the code, or from the
'jksrc.zip' code?

- If you just need the genome browser web server, I would follow the
instructions for step 6(a) to get the cgi-bin binaries (on
/admin/mirror.html) and forget about CVS or the source.

- If you need all the command-line programs, i would get the source
which is released as a .zip file, follow instructions for first choice
on step 6(d) "Download the released zipped version of the source" also
see the README in the zip.

We need to review the mirror procedure instructions.

Cheers
Mike.



On Fri, Jul 25, 2008 at 12:40 PM, Ann Zweig <ann at soe.ucsc.edu> wrote:
> Hi Kotien,
>
>        A developer here proposes that the rsync error isn't really an error.  If you
> 'man rsync', you'll see it requires a SRC and DEST argument.  You removed
> the SRC part of the rsync arguments, hence the rsync error.
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
>
> Ann Zweig wrote:
>> Hello again, Kotien,
>>
>> The makefile in kent/src/utils uses the SCRIPTS make variable.  You will need to
>> override that like so:
>>
>>       cd kent/src/scripts
>>       make SCRIPTS=/a/directory/here alpha
>>
>> You should use a directory that's already in your path environment variable,
>> e.g. /usr/local/bin.
>>
>>       We are still looking into the rsync error.
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu
>>
>>
>>
>>
>>
>> Wu, Kotien (NIH/NCI) [E] wrote:
>>> It looks that I hit the new problem:
>>>
>>> bash-3.00# pwd
>>> /app1/data10/intel/jksrc/kent/src/utils
>>> bash-3.00# make scripts
>>> cp -p agpToLift /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p iSync /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p lodToBedScore /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p mkMafFrames.pl /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> make: *** [scripts] Error 1
>>>
>>> or
>>>
>>> bash-3.00# make alpha
>>> cp -p agpToLift /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p iSync /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p lodToBedScore /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p mkMafFrames.pl /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> make: *** [scripts] Error 1
>>>
>>>
>>> In our root, we don't have dir cluster/bin.
>>>
>>> Do I need to create dir cluster/bin at root dir?
>>>
>>> Also how about error message:
>>> rsync error: syntax or usage error (code 1) at main.c(891)
>>>
>>> which came out even I comment out cvsFiles stuff.
>>>
>>> Many thanks!
>>>
>>> Kotien
>>>
>>> -----Original Message-----
>>> From: Ann Zweig [mailto:ann at soe.ucsc.edu]
>>> Sent: Friday, July 25, 2008 12:33 PM
>>> To: Wu, Kotien (NIH/NCI) [E]
>>> Cc: genome-mirror at cse.ucsc.edu
>>> Subject: Re: [Genome-mirror] make installation in kent/src/hg/js
>>>
>>> Hello Kotien,
>>>
>>>      It appears that this new step hasn't been added to our mirror
>>> procedures help
>>> page yet: http://genome.ucsc.edu/admin/mirror.html
>>>
>>>      I will explain here what you need to to.
>>>
>>> The cvsFiles lives here:  kent/src/utils/cvsTools/cvsFiles
>>>
>>> It is installed when one runs 'make scripts' or 'make alpha' in
>>> kent/src/utils/.  Unfortunately kent/src/makefile invokes plain old
>>> 'make'
>>> in utils -- for 'make', but not for 'make alpha', in kent/src.  Bottom
>>> line is, a top-level build does not install cvsFiles in BINDIR but it
>>> should.
>>>
>>>
>>>
>>> Regards,
>>>
>>> ----------
>>> Ann Zweig
>>> UCSC Genome Bioinformatics Group
>>> http://genome.ucsc.edu
>>>
>>>
>>>
>>> Wu, Kotien (NIH/NCI) [E] wrote:
>>>> Our machine is x86_64 GNU/Linux.
>>>>
>>>>
>>>>
>>>> When we do installation in kent/src/hg/js
>>>>
>>>>
>>>>
>>>> run
>>>>
>>>>
>>>>
>>>> doInstall:
>>>>
>>>>         @mkdir -p ${DEST}/
>>>>
>>>>         rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
>>>> ${DEST}/
>>>>
>>>>
>>>>
>>>> in the makefile over there.
>>>>
>>>>
>>>>
>>>> we got
>>>>
>>>>
>>>>
>>>> make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'
>>>>
>>>> rsync -t -r --relative --exclude='makefile'  `cvsFiles`
>>>> /usr/local/apache/htdocs/js/
>>>>
>>>> /bin/sh: cvsFiles: command not found
>>>>
>>>> rsync  version 2.6.3  protocol version 28
>>>>
>>>> Copyright (C) 1996-2004 by Andrew Tridgell and others
>>>>
>>>> <http://rsync.samba.org/>
>>>>
>>>>
>>>>
>>>> ......
>>>>
>>>>
>>>>
>>>> Please see the rsync(1) and rsyncd.conf(5) man pages for full
>>>> documentation
>>>>
>>>> See http://rsync.samba.org/ for updates, bug reports, and answers
>>>>
>>>> rsync error: syntax or usage error (code 1) at main.c(891)
>>>>
>>>> make[2]: *** [doInstall] Error 1
>>>>
>>>>
>>>>
>>>> If I comment out ${EXCL} `cvsFiles` and run as
>>>>
>>>>
>>>>
>>>> doInstall:
>>>>
>>>>         @mkdir -p ${DEST}/
>>>>
>>>>         rsync -t -r --relative --exclude='makefile' ${DEST}/
>>>>
>>>>         ## rsync -t -r --relative --exclude='makefile' ${EXCL}
>>>> `cvsFiles` ${DEST}/
>>>>
>>>>
>>>>
>>>> We got similar error message without '/bin/sh: cvsFiles: command not
>>>> found'.
>>>>
>>>>
>>>>
>>>> Could you please help us, what we need to do?
>>>>
>>>>
>>>>
>>>> Thanks a lot!
>>>>
>>>>
>>>>
>>>> Kotien
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Genome-mirror mailing list
>>>> Genome-mirror at soe.ucsc.edu
>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>> _______________________________________________
>> Genome-mirror mailing list
>> Genome-mirror at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>



-- 
Michael Pheasant
Associate Project Scientist
UCSC Genome Browser

Email: mikep at soe.ucsc.edu
Skype: mpheasant at skype.com
Phone: +1-831-706-2689
ll=36.953713,-122.033153

Location: Engineering2 Room 515
Post: CBSE, UC Santa Cruz, MS:CBSE/ITI
1156 High Street
Santa Cruz, CA 95064, USA

From wuko at mail.nih.gov  Fri Jul 25 13:37:41 2008
From: wuko at mail.nih.gov (Wu, Kotien (NIH/NCI) [E])
Date: Fri, 25 Jul 2008 16:37:41 -0400
Subject: [Genome-mirror] make installation in kent/src/hg/js
References: <D54AB1BFDE02B9449144D34E6F58499C02CC3720@nihcesmlbx10.nih.gov>
	<488A1C68.6000407@soe.ucsc.edu> <488A2C12.1080503@soe.ucsc.edu>
Message-ID: <D54AB1BFDE02B9449144D34E6F58499C01D17AB6@nihcesmlbx10.nih.gov>

Thanks a lot!
 
It looks EXCL has not be defined and what I should put.
 
Kotien

________________________________

From: Ann Zweig [mailto:ann at soe.ucsc.edu]
Sent: Fri 7/25/2008 3:40 PM
To: Wu, Kotien (NIH/NCI) [E]
Cc: genome-mirror at cse.ucsc.edu
Subject: Re: [Genome-mirror] make installation in kent/src/hg/js



Hi Kotien,

        A developer here proposes that the rsync error isn't really an error.  If you
'man rsync', you'll see it requires a SRC and DEST argument.  You removed
the SRC part of the rsync arguments, hence the rsync error.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu <http://genome.ucsc.edu/> 



Ann Zweig wrote:
> Hello again, Kotien,
>
> The makefile in kent/src/utils uses the SCRIPTS make variable.  You will need to
> override that like so:
>
>       cd kent/src/scripts
>       make SCRIPTS=/a/directory/here alpha
>
> You should use a directory that's already in your path environment variable,
> e.g. /usr/local/bin.
>
>       We are still looking into the rsync error.
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu <http://genome.ucsc.edu/> 
>
>
>
>
>
> Wu, Kotien (NIH/NCI) [E] wrote:
>> It looks that I hit the new problem:
>>
>> bash-3.00# pwd
>> /app1/data10/intel/jksrc/kent/src/utils
>> bash-3.00# make scripts
>> cp -p agpToLift /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p iSync /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p lodToBedScore /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p mkMafFrames.pl /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> make: *** [scripts] Error 1
>>
>> or
>>
>> bash-3.00# make alpha
>> cp -p agpToLift /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p iSync /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p lodToBedScore /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> cp -p mkMafFrames.pl /cluster/bin/scripts
>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>> directory
>> make: *** [scripts] Error 1
>>
>>
>> In our root, we don't have dir cluster/bin.
>>
>> Do I need to create dir cluster/bin at root dir?
>>
>> Also how about error message:
>> rsync error: syntax or usage error (code 1) at main.c(891)
>>
>> which came out even I comment out cvsFiles stuff.
>>
>> Many thanks!
>>
>> Kotien
>>
>> -----Original Message-----
>> From: Ann Zweig [mailto:ann at soe.ucsc.edu]
>> Sent: Friday, July 25, 2008 12:33 PM
>> To: Wu, Kotien (NIH/NCI) [E]
>> Cc: genome-mirror at cse.ucsc.edu
>> Subject: Re: [Genome-mirror] make installation in kent/src/hg/js
>>
>> Hello Kotien,
>>
>>      It appears that this new step hasn't been added to our mirror
>> procedures help
>> page yet: http://genome.ucsc.edu/admin/mirror.html
>>
>>      I will explain here what you need to to.
>>
>> The cvsFiles lives here:  kent/src/utils/cvsTools/cvsFiles
>>
>> It is installed when one runs 'make scripts' or 'make alpha' in
>> kent/src/utils/.  Unfortunately kent/src/makefile invokes plain old
>> 'make'
>> in utils -- for 'make', but not for 'make alpha', in kent/src.  Bottom
>> line is, a top-level build does not install cvsFiles in BINDIR but it
>> should.     
>>
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu <http://genome.ucsc.edu/> 
>>
>>
>>
>> Wu, Kotien (NIH/NCI) [E] wrote:
>>> Our machine is x86_64 GNU/Linux.
>>>
>>> 
>>>
>>> When we do installation in kent/src/hg/js
>>>
>>> 
>>>
>>> run
>>>
>>> 
>>>
>>> doInstall:
>>>
>>>         @mkdir -p ${DEST}/
>>>
>>>         rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
>>> ${DEST}/
>>>
>>> 
>>>
>>> in the makefile over there.
>>>
>>> 
>>>
>>> we got
>>>
>>> 
>>>
>>> make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'
>>>
>>> rsync -t -r --relative --exclude='makefile'  `cvsFiles`
>>> /usr/local/apache/htdocs/js/
>>>
>>> /bin/sh: cvsFiles: command not found
>>>
>>> rsync  version 2.6.3  protocol version 28
>>>
>>> Copyright (C) 1996-2004 by Andrew Tridgell and others
>>>
>>> <http://rsync.samba.org/>
>>>
>>> 
>>>
>>> ......
>>>
>>> 
>>>
>>> Please see the rsync(1) and rsyncd.conf(5) man pages for full
>>> documentation
>>>
>>> See http://rsync.samba.org/ for updates, bug reports, and answers
>>>
>>> rsync error: syntax or usage error (code 1) at main.c(891)
>>>
>>> make[2]: *** [doInstall] Error 1
>>>
>>> 
>>>
>>> If I comment out ${EXCL} `cvsFiles` and run as
>>>
>>> 
>>>
>>> doInstall:
>>>
>>>         @mkdir -p ${DEST}/
>>>
>>>         rsync -t -r --relative --exclude='makefile' ${DEST}/
>>>
>>>         ## rsync -t -r --relative --exclude='makefile' ${EXCL}
>>> `cvsFiles` ${DEST}/
>>>
>>> 
>>>
>>> We got similar error message without '/bin/sh: cvsFiles: command not
>>> found'.
>>>
>>> 
>>>
>>> Could you please help us, what we need to do?
>>>
>>> 
>>>
>>> Thanks a lot!
>>>
>>> 
>>>
>>> Kotien
>>>
>>> 
>>>
>>> _______________________________________________
>>> Genome-mirror mailing list
>>> Genome-mirror at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror




From wuko at mail.nih.gov  Fri Jul 25 13:43:10 2008
From: wuko at mail.nih.gov (Wu, Kotien (NIH/NCI) [E])
Date: Fri, 25 Jul 2008 16:43:10 -0400
Subject: [Genome-mirror] make installation in kent/src/hg/js
References: <D54AB1BFDE02B9449144D34E6F58499C02CC3720@nihcesmlbx10.nih.gov><488A1C68.6000407@soe.ucsc.edu>
	<488A2C12.1080503@soe.ucsc.edu>
	<61ee49d20807251310p5c98fcfbo2dc9d0d1946a34a7@mail.gmail.com>
Message-ID: <D54AB1BFDE02B9449144D34E6F58499C01D17AB5@nihcesmlbx10.nih.gov>

We need the source and then put some our thing into there:
 
http://cgwb.nci.nih.gov
 
We unzipped jksrc.zip and everything is OK, like we did before, except new stuff rsync.
 
I will follow Ann's instruction to try rsync next Thursday.
 
Many thanks!
 
Kotien

________________________________

From: Michael Pheasant [mailto:mikep at soe.ucsc.edu]
Sent: Fri 7/25/2008 4:10 PM
To: Wu, Kotien (NIH/NCI) [E]
Cc: genome-mirror at cse.ucsc.edu
Subject: Re: [Genome-mirror] make installation in kent/src/hg/js



Hi Kotien

Are you making a mirror using a CVS version of the code, or from the
'jksrc.zip' code?

- If you just need the genome browser web server, I would follow the
instructions for step 6(a) to get the cgi-bin binaries (on
/admin/mirror.html) and forget about CVS or the source.

- If you need all the command-line programs, i would get the source
which is released as a .zip file, follow instructions for first choice
on step 6(d) "Download the released zipped version of the source" also
see the README in the zip.

We need to review the mirror procedure instructions.

Cheers
Mike.



On Fri, Jul 25, 2008 at 12:40 PM, Ann Zweig <ann at soe.ucsc.edu> wrote:
> Hi Kotien,
>
>        A developer here proposes that the rsync error isn't really an error.  If you
> 'man rsync', you'll see it requires a SRC and DEST argument.  You removed
> the SRC part of the rsync arguments, hence the rsync error.
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu <http://genome.ucsc.edu/> 
>
>
>
> Ann Zweig wrote:
>> Hello again, Kotien,
>>
>> The makefile in kent/src/utils uses the SCRIPTS make variable.  You will need to
>> override that like so:
>>
>>       cd kent/src/scripts
>>       make SCRIPTS=/a/directory/here alpha
>>
>> You should use a directory that's already in your path environment variable,
>> e.g. /usr/local/bin.
>>
>>       We are still looking into the rsync error.
>>
>>
>> Regards,
>>
>> ----------
>> Ann Zweig
>> UCSC Genome Bioinformatics Group
>> http://genome.ucsc.edu <http://genome.ucsc.edu/> 
>>
>>
>>
>>
>>
>> Wu, Kotien (NIH/NCI) [E] wrote:
>>> It looks that I hit the new problem:
>>>
>>> bash-3.00# pwd
>>> /app1/data10/intel/jksrc/kent/src/utils
>>> bash-3.00# make scripts
>>> cp -p agpToLift /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p iSync /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p lodToBedScore /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p mkMafFrames.pl /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> make: *** [scripts] Error 1
>>>
>>> or
>>>
>>> bash-3.00# make alpha
>>> cp -p agpToLift /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p iSync /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p lodToBedScore /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> cp -p mkMafFrames.pl /cluster/bin/scripts
>>> cp: cannot create regular file `/cluster/bin/scripts': No such file or
>>> directory
>>> make: *** [scripts] Error 1
>>>
>>>
>>> In our root, we don't have dir cluster/bin.
>>>
>>> Do I need to create dir cluster/bin at root dir?
>>>
>>> Also how about error message:
>>> rsync error: syntax or usage error (code 1) at main.c(891)
>>>
>>> which came out even I comment out cvsFiles stuff.
>>>
>>> Many thanks!
>>>
>>> Kotien
>>>
>>> -----Original Message-----
>>> From: Ann Zweig [mailto:ann at soe.ucsc.edu]
>>> Sent: Friday, July 25, 2008 12:33 PM
>>> To: Wu, Kotien (NIH/NCI) [E]
>>> Cc: genome-mirror at cse.ucsc.edu
>>> Subject: Re: [Genome-mirror] make installation in kent/src/hg/js
>>>
>>> Hello Kotien,
>>>
>>>      It appears that this new step hasn't been added to our mirror
>>> procedures help
>>> page yet: http://genome.ucsc.edu/admin/mirror.html
>>>
>>>      I will explain here what you need to to.
>>>
>>> The cvsFiles lives here:  kent/src/utils/cvsTools/cvsFiles
>>>
>>> It is installed when one runs 'make scripts' or 'make alpha' in
>>> kent/src/utils/.  Unfortunately kent/src/makefile invokes plain old
>>> 'make'
>>> in utils -- for 'make', but not for 'make alpha', in kent/src.  Bottom
>>> line is, a top-level build does not install cvsFiles in BINDIR but it
>>> should.
>>>
>>>
>>>
>>> Regards,
>>>
>>> ----------
>>> Ann Zweig
>>> UCSC Genome Bioinformatics Group
>>> http://genome.ucsc.edu <http://genome.ucsc.edu/> 
>>>
>>>
>>>
>>> Wu, Kotien (NIH/NCI) [E] wrote:
>>>> Our machine is x86_64 GNU/Linux.
>>>>
>>>>
>>>>
>>>> When we do installation in kent/src/hg/js
>>>>
>>>>
>>>>
>>>> run
>>>>
>>>>
>>>>
>>>> doInstall:
>>>>
>>>>         @mkdir -p ${DEST}/
>>>>
>>>>         rsync -t -r --relative --exclude='makefile' ${EXCL} `cvsFiles`
>>>> ${DEST}/
>>>>
>>>>
>>>>
>>>> in the makefile over there.
>>>>
>>>>
>>>>
>>>> we got
>>>>
>>>>
>>>>
>>>> make[2]: Entering directory `/app1/data10/intel/jksrc/kent/src/hg/js'
>>>>
>>>> rsync -t -r --relative --exclude='makefile'  `cvsFiles`
>>>> /usr/local/apache/htdocs/js/
>>>>
>>>> /bin/sh: cvsFiles: command not found
>>>>
>>>> rsync  version 2.6.3  protocol version 28
>>>>
>>>> Copyright (C) 1996-2004 by Andrew Tridgell and others
>>>>
>>>> <http://rsync.samba.org/>
>>>>
>>>>
>>>>
>>>> ......
>>>>
>>>>
>>>>
>>>> Please see the rsync(1) and rsyncd.conf(5) man pages for full
>>>> documentation
>>>>
>>>> See http://rsync.samba.org/ for updates, bug reports, and answers
>>>>
>>>> rsync error: syntax or usage error (code 1) at main.c(891)
>>>>
>>>> make[2]: *** [doInstall] Error 1
>>>>
>>>>
>>>>
>>>> If I comment out ${EXCL} `cvsFiles` and run as
>>>>
>>>>
>>>>
>>>> doInstall:
>>>>
>>>>         @mkdir -p ${DEST}/
>>>>
>>>>         rsync -t -r --relative --exclude='makefile' ${DEST}/
>>>>
>>>>         ## rsync -t -r --relative --exclude='makefile' ${EXCL}
>>>> `cvsFiles` ${DEST}/
>>>>
>>>>
>>>>
>>>> We got similar error message without '/bin/sh: cvsFiles: command not
>>>> found'.
>>>>
>>>>
>>>>
>>>> Could you please help us, what we need to do?
>>>>
>>>>
>>>>
>>>> Thanks a lot!
>>>>
>>>>
>>>>
>>>> Kotien
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Genome-mirror mailing list
>>>> Genome-mirror at soe.ucsc.edu
>>>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>> _______________________________________________
>> Genome-mirror mailing list
>> Genome-mirror at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror
>



--
Michael Pheasant
Associate Project Scientist
UCSC Genome Browser

Email: mikep at soe.ucsc.edu
Skype: mpheasant at skype.com
Phone: +1-831-706-2689
ll=36.953713,-122.033153

Location: Engineering2 Room 515
Post: CBSE, UC Santa Cruz, MS:CBSE/ITI
1156 High Street
Santa Cruz, CA 95064, USA




From hooverdm at helix.nih.gov  Thu Jul 31 06:57:37 2008
From: hooverdm at helix.nih.gov (David Hoover)
Date: Thu, 31 Jul 2008 09:57:37 -0400
Subject: [Genome-mirror] MGI Phenotype for mm9
Message-ID: <4891C4D1.8090705@helix.nih.gov>

When will the MGI Phenotype track for mm9 be publicly available?

David Hoover, Helix Systems Staff, CIT/NIH

From zlei at chgc.sh.cn  Thu Jul 31 01:17:48 2008
From: zlei at chgc.sh.cn (zlei)
Date: Thu, 31 Jul 2008 16:17:48 +0800
Subject: [Genome-mirror] help
Message-ID: <20080731081750.56C3D528449@mail.chgc.sh.cn>

Dear sir?

Thank you for taking you time to see my letter.

When I localsation you software of Gene Browser,I meet some problems as I
followed the step in the web (http://genome.ucsc.edu/admin/jk-install.html).
But when I carry the step 7 , Go to the kent/src/hg directory and type: make
compile.The problem is coming like that :

 

collect2: ld returned 1 exit status

make[1]: *** [compile] Error 1

make[1]: Leaving directory `/home/schi/jkscr/kent/src/hg/makeDb/hgLoadMaf'

make: *** [install] Error 2

 

Thank you for you relay.Please soon.

 
Yours  zhaolei


From ann at soe.ucsc.edu  Thu Jul 31 10:10:43 2008
From: ann at soe.ucsc.edu (Ann Zweig)
Date: Thu, 31 Jul 2008 10:10:43 -0700
Subject: [Genome-mirror] MGI Phenotype for mm9
In-Reply-To: <4891C4D1.8090705@helix.nih.gov>
References: <4891C4D1.8090705@helix.nih.gov>
Message-ID: <4891F213.3090205@soe.ucsc.edu>

Hello David,

	That track was released a few days ago.  Check in the "Phenotype and Allele" 
group of track controls.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



David Hoover wrote:
> When will the MGI Phenotype track for mm9 be publicly available?
> 
> David Hoover, Helix Systems Staff, CIT/NIH
> _______________________________________________
> Genome-mirror mailing list
> Genome-mirror at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome-mirror

From hiram at soe.ucsc.edu  Thu Jul 31 10:12:56 2008
From: hiram at soe.ucsc.edu (Hiram Clawson)
Date: Thu, 31 Jul 2008 10:12:56 -0700
Subject: [Genome-mirror] help
In-Reply-To: <20080731081750.56C3D528449@mail.chgc.sh.cn>
References: <20080731081750.56C3D528449@mail.chgc.sh.cn>
Message-ID: <4891F298.2010403@soe.ucsc.edu>

Good Morning Zhaolei:

Please continue reading the instructions in the source tree:
	src/product/README.building.source

--Hiram

zlei wrote:
> Dear sir??
> 
> Thank you for taking you time to see my letter.
> 
> When I localsation you software of Gene Browser,I meet some problems as I
> followed the step in the web (http://genome.ucsc.edu/admin/jk-install.html).
> But when I carry the step 7 , Go to the kent/src/hg directory and type: make
> compile.The problem is coming like that :
> 
> collect2: ld returned 1 exit status
> 
> make[1]: *** [compile] Error 1
> 
> make[1]: Leaving directory `/home/schi/jkscr/kent/src/hg/makeDb/hgLoadMaf'
> 
> make: *** [install] Error 2
>  
> Thank you for you relay.Please soon.
>  
> Yours  zhaolei