v286 Genome Browser Available

[Chin Li]

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

or labelled with source number:
http://hgdownload.soe.ucsc.edu/admin/jksrc.v286.zip

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

Summaries of changes can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgc hgPal hgEncodeVocab
hgBlat hgConvert hgCustom hgFileSearch hgFileUi hgGateway
hgGene hgGenome hgHubConnect hgLiftOver hgLogin hgNear hgPcr
hgSession hgTables hgTracks hgTrackUi hgUserSuggestion hgVai
hgVisiGene mkEncodeFrameset hgEncodeDataVersions phyloGif
hgSuggest hgApi hgEncodeApi hgRenderTracks

and these configuration files:

/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/cgi-bin/lsSnpPdbChimera.py
/usr/local/apache/cgi-bin/greatData/*
/usr/local/apache/cgi-bin/encode/cv.ra

Please rsync --delete these directories:

/usr/local/apache/htdocs/js/*
/usr/local/apache/htdocs/style/*

Please rsync this directory:
/usr/local/apache/htdocs/images/*

A new hgcentral.sql file should now be present at:
http://hgdownload.cse.ucsc.edu/admin/

If you have any questions or concerns, please feel free to write back
to this mail list.

Thanks,
Chin

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

Please note, for this version v288 release, our development server
has updated to a newer version of CentOS (6.4). Consequently, this
CGI build is dependent on some of the libraries in this environment.
If your standard update procedure is to use our pre-built CGI binaries,
they may not function in your environment. You will need to build
the CGI binaries in your environment from the source. As a temporary
measure, we have left the v287 CGI binaries at:
ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin.v287/
The version v288 binaries can be found at:
ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

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

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v288.zip

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

Summaries of changes can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgc hgPal hgEncodeVocab
hgBlat hgConvert hgCustom hgFileSearch hgFileUi hgGateway
hgGene hgGenome hgHubConnect hgLiftOver hgLogin hgNear hgPcr
hgSession hgTables hgTracks hgTrackUi hgUserSuggestion hgVai

hgVisiGene hgEncodeDataVersions phyloGif

hgSuggest hgApi hgEncodeApi hgRenderTracks

and these configuration files:

/usr/local/apache/cgi-bin/all.joiner

/usr/local/apache/cgi-bin/encode/cv.ra
/usr/local/apache/cgi-bin/greatData/*
/usr/local/apache/cgi-bin/hgCgiData/*
/usr/local/apache/cgi-bin/hgGeneData/*
/usr/local/apache/cgi-bin/hgNearData/*
/usr/local/apache/cgi-bin/hgcData/*
/usr/local/apache/cgi-bin/loader/*
/usr/local/apache/cgi-bin/lsSnpPdbChimera.py
/usr/local/apache/cgi-bin/visiGeneData/*

Please rsync --delete these directories:

/usr/local/apache/htdocs/js/*
/usr/local/apache/htdocs/style/*

Please rsync this directory:
/usr/local/apache/htdocs/images/*

The script in the source tree: src/product/scripts/updateHtml.sh
can be used to update your htdocs directory.

A new hgcentral.sql file is now be present at:

http://hgdownload.cse.ucsc.edu/admin/

If you have any questions or concerns, please feel free to write back
to this mail list.

Thanks, Hiram

[Daofeng Li]

Hi Hiram,

I would like to run `git pull` to update our local mirror, while the `git pull` command get no response for quite a long time.

I could be able to git other repository, is it possible there is a problem with the UCSC server side? Would you please look into it?

Thanks a lot.

Daofeng

--

To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirror+unsubscribe@soe.ucsc.edu.

[Hiram Clawson]

Good Morning Daofeng:

We had a glitch with our public git server.
It should be back in operation at this time.
Verify your git server is correct: 'git config -l'
indicates: git://genome-source.cse.ucsc.edu/kent.git
and it resolves to:

$ host genome-source.cse.ucsc.edu
genome-source.cse.ucsc.edu is an alias for hgwdev.sdsc.edu.
hgwdev.sdsc.edu has address 132.249.245.79

--Hiram

On 8/28/13 6:36 AM, Daofeng Li wrote:
> Hi Hiram,
>
> I would like to run `git pull` to update our local mirror, while the `git
> pull` command get no response for quite a long time.
> I could be able to git other repository, is it possible there is a problem
> with the UCSC server side? Would you please look into it?
>
> Thanks a lot.
>
> Daofeng
>
>
> On Tue, Aug 27, 2013 at 6:07 PM, Hiram Clawson <hi...@soe.ucsc.edu> wrote:
>
>> Good Afternoon Genome Browser Mirror Site Operators:
>>
>> Please note, for this version v288 release, our development server
>> has updated to a newer version of CentOS (6.4). Consequently, this
>> CGI build is dependent on some of the libraries in this environment.
>> If your standard update procedure is to use our pre-built CGI binaries,
>> they may not function in your environment. You will need to build
>> the CGI binaries in your environment from the source. As a temporary
>> measure, we have left the v287 CGI binaries at:

>> ftp://hgdownload.cse.ucsc.edu/**apache/cgi-bin.v287/<ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin.v287/>

>> The version v288 binaries can be found at:

>> ftp://hgdownload.cse.ucsc.edu/**apache/cgi-bin/<ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/>

>>
>> The source is now available at:

>> http://hgdownload.soe.ucsc.**edu/admin/jksrc.zip<http://hgdownload.soe.ucsc.edu/admin/jksrc.zip>

>>
>> or labelled with source number:

>> http://hgdownload.soe.ucsc.**edu/admin/jksrc.v288.zip<http://hgdownload.soe.ucsc.edu/admin/jksrc.v288.zip>

>>
>> A license is required for commercial download and/or installation of
>> the Genome Browser binaries and source code. No license is needed for
>> academic, nonprofit, and personal use.
>>
>> Summaries of changes can be found here:

>> http://genecats.soe.ucsc.edu/**builds/versions.html<http://genecats.soe.ucsc.edu/builds/versions.html>

>>
>> The following CGIs were updated:
>>
>> cartDump cartReset das hgc hgPal hgEncodeVocab
>> hgBlat hgConvert hgCustom hgFileSearch hgFileUi hgGateway
>> hgGene hgGenome hgHubConnect hgLiftOver hgLogin hgNear hgPcr
>> hgSession hgTables hgTracks hgTrackUi hgUserSuggestion hgVai
>> hgVisiGene hgEncodeDataVersions phyloGif
>> hgSuggest hgApi hgEncodeApi hgRenderTracks
>>
>> and these configuration files:
>>

>> /usr/local/apache/cgi-bin/all.**joiner
>> /usr/local/apache/cgi-bin/**encode/cv.ra
>> /usr/local/apache/cgi-bin/**greatData/*
>> /usr/local/apache/cgi-bin/**hgCgiData/*
>> /usr/local/apache/cgi-bin/**hgGeneData/*
>> /usr/local/apache/cgi-bin/**hgNearData/*
>> /usr/local/apache/cgi-bin/**hgcData/*
>> /usr/local/apache/cgi-bin/**loader/*
>> /usr/local/apache/cgi-bin/**lsSnpPdbChimera.py
>> /usr/local/apache/cgi-bin/**visiGeneData/*

>>
>> Please rsync --delete these directories:
>>
>> /usr/local/apache/htdocs/js/*

>> /usr/local/apache/htdocs/**style/*
>>
>> Please rsync this directory:
>> /usr/local/apache/htdocs/**images/*
>>
>> The script in the source tree: src/product/scripts/**updateHtml.sh

>> can be used to update your htdocs directory.
>>
>> A new hgcentral.sql file is now be present at:

>> http://hgdownload.cse.ucsc.**edu/admin/<http://hgdownload.cse.ucsc.edu/admin/>

>>
>> If you have any questions or concerns, please feel free to write back
>> to this mail list.
>>
>> Thanks, Hiram
>>
>> --
>>
>> To unsubscribe from this group and stop receiving emails from it, send an

>> email to genome-mirror+unsubscribe@soe.**ucsc.edu<genome-mirror%2Bunsu...@soe.ucsc.edu>
>> .
>>
>

[Daofeng Li]

Hi Hiram,

Thanks a lot for your response.

Seems I am using the right git server, while the `git pull` still get no response....

$ git config -l

user.name=Daofeng Li

user.email=lid...@gmail.com

color.status=auto

color.branch=auto

color.ui=auto

core.repositoryformatversion=0

core.filemode=true

core.bare=false

core.logallrefupdates=true

remote.origin.fetch=+refs/heads/*:refs/remotes/origin/*

remote.origin.url=git://genome-source.cse.ucsc.edu/kent.git

branch.master.remote=origin

branch.master.merge=refs/heads/master

branch.beta.remote=origin

branch.beta.merge=refs/heads/beta

$ host genome-source.cse.ucsc.edu

genome-source.cse.ucsc.edu is an alias for hgwdev.sdsc.edu.

hgwdev.sdsc.edu has address 132.249.245.79

$ git pull

(long time no response)

Did I do something wrong?

Thanks again,

Daofeng

[Hiram Clawson]

Good Morning Daofeng:

Did you have firewall policies change at your institution ?
We have verified the git server is functioning at outside
locations and is correctly serving the v288/beta release.

You could run an 'strace' on the command to see where it gets stuck:

$ strace -f git pull > strace.log 2>&1

Then watch the strace.log to see what system call may be waiting.

--Hiram

On 8/28/13 12:51 PM, Daofeng Li wrote:
> Hi Hiram,
>

>> indicates: git://genome-source.cse.ucsc.**edu/kent.git<http://genome-source.cse.ucsc.edu/kent.git>

[Hiram Clawson]

Sounds like firewall issues, try it with the http protocol:

git clone http://genome-source.cse.ucsc.edu/kent.git

to eliminate the git protocol firewall situation.

On 8/29/13 1:45 PM, Daofeng Li wrote:
> Hello Hiram,
>
> Now I am getting following error with clone:
>
> $ git clone git://genome-source.cse.ucsc.edu/kent.git
> Cloning into 'kent'...
> fatal: read error: Connection reset by peer
>
> with pull:
> $ git pull
> fatal: read error: Connection timed out
>
>
> Thanks for your response. The strace.log file was quite huge, if you want I
> can send it to you.
> I will also try to contact our system admim. Thanks.
>
>
>
> Daofeng

>
>
> On Thu, Aug 29, 2013 at 2:05 PM, Hiram Clawson <hi...@soe.ucsc.edu> wrote:
>
>> Good Morning Daofeng:
>>

>> Did you have firewall policies change at your institution ?
>> We have verified the git server is functioning at outside
>> locations and is correctly serving the v288/beta release.
>>
>> You could run an 'strace' on the command to see where it gets stuck:
>>
>> $ strace -f git pull > strace.log 2>&1
>>
>> Then watch the strace.log to see what system call may be waiting.
>>
>> --Hiram
>>
>>
>> On 8/28/13 12:51 PM, Daofeng Li wrote:
>>
>>> Hi Hiram,
>>>
>>> Thanks a lot for your response.
>>>
>>> Seems I am using the right git server, while the `git pull` still get no
>>> response....
>>>
>>> $ git config -l
>>> user.name=Daofeng Li
>>> user.email=lid...@gmail.com
>>> color.status=auto
>>> color.branch=auto
>>> color.ui=auto
>>> core.repositoryformatversion=0
>>> core.filemode=true
>>> core.bare=false
>>> core.logallrefupdates=true

>>> remote.origin.fetch=+refs/**heads/*:refs/remotes/origin/*
>>> remote.origin.url=git://genome**-source.cse.ucsc.edu/kent.git<http://genome-source.cse.ucsc.edu/kent.git>
>>> branch.master.remote=origin
>>> branch.master.merge=refs/**heads/master
>>> branch.beta.remote=origin
>>> branch.beta.merge=refs/heads/**beta

>>>
>>> $ host genome-source.cse.ucsc.edu
>>> genome-source.cse.ucsc.edu is an alias for hgwdev.sdsc.edu.
>>> hgwdev.sdsc.edu has address 132.249.245.79
>>>
>>> $ git pull
>>>
>>> (long time no response)
>>>
>>> Did I do something wrong?
>>>
>>> Thanks again,
>>>
>>>
>>> Daofeng
>>>
>>>
>>> On Wed, Aug 28, 2013 at 2:13 PM, Hiram Clawson <hi...@soe.ucsc.edu>
>>> wrote:
>>>
>>> Good Morning Daofeng:
>>>>
>>>> We had a glitch with our public git server.
>>>> It should be back in operation at this time.
>>>> Verify your git server is correct: 'git config -l'

>>>> indicates: git://genome-source.cse.ucsc.****edu/kent.git<http://genome-*
>>>> *source.cse.ucsc.edu/kent.git<http://genome-source.cse.ucsc.edu/kent.git>

[Daofeng Li]

Hello Hiram,

Now I am getting following error with clone:

$ git clone git://genome-source.cse.ucsc.edu/kent.git

Cloning into 'kent'...

fatal: read error: Connection reset by peer

with pull:

$ git pull

fatal: read error: Connection timed out

Thanks for your response. The strace.log file was quite huge, if you want I can send it to you.

I will also try to contact our system admim. Thanks.

Daofeng

[Galt Barber]

You can also test for basic working git connectivity this way:

git ls-remote git://genome-source.cse.ucsc.edu/kent.git

or

git ls-remote http://genome-source.cse.ucsc.edu/kent.git

If it works, you get a dump of some branches that are available.

Of course you are interested in the beta branch which contains
the latest official release of the UCSC genome browser software.

Of course, if it doesn't work, one usually suspects network problems
like firewall or proxy.

-Galt

--

[Daofeng Li]

Thank you Galt and Hiram.

The http link works for me...

Best,

Daofeng

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v289 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v289.zip

The version v289 CGI binaries can be found at:
ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v290 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v290.zip

The version v290 CGI binaries can be found at:

Thanks, Hiram

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v291 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v291.zip

The version v291 CGI binaries can be found at:

[David Hoover]

I think there is a file missing from hgTables:

hal.c:10:25: error: halBlockViz.h: No such file or directory

David Hoover
Helix Systems Staff

[Hiram Clawson]

Good Morning David:

Check src/inc/common.mk
It shouldn't be turning on USE_HAL=1
Try adding an 'undef USE_HAL'
in there to get rid of that requirement.

[Hiram Clawson]

My previous suggestion is a dead end. There is broken
code in the hgTables directory. I'll see we can get this
fixed.

--Hiram

On 10/31/13 10:34 AM, David Hoover wrote:

[David Hoover]

Is HAL required? Should I install it locally?

[Hiram Clawson]

It isn't required, but it is really cool.
We need to deliver source that doesn't need it.
I'm not sure how well the public HAL source would
mesh with our business. We are helping develop
this business.

--Hiram

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v292 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v292.zip

The version v292 CGI binaries can be found at:
rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

Summaries of changes can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene
hgGenome hgHubConnect hgLiftOver hgLogin hgNear hgPal hgPcr hgRenderTracks
hgSession hgSuggest hgTables hgTrackUi hgTracks hgUserSuggestion hgVai
hgVisiGene hgc phyloGif

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v293 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v293.zip

The version v293 CGI binaries can be found at:

[Hiram Clawson]

Good Evening Genome Browser Mirror Site Operators:

The version v294 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v294.zip

The version v294 CGI binaries can be found at:

A new hgcentral.sql file is now available at:

http://hgdownload.cse.ucsc.edu/admin/

If you have any questions or concerns, please feel free to write back

to this genome-mirror mail list.

Thanks, Hiram

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v295 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v295.zip

The version v295 CGI binaries can be found at:

[OW Jack Ling (GIS)]

Hi Hiram,

What is the mediawiki version that UCSC Genome Browser version 295 is compatible with ? I'm still having mediawiki 1.16 that is compatible with my current UCSC Genome Browser version 262. Do I need to upgrade it ?

Is the mysql database difference between latest version and version 262 only affecting the hgcentral database ?

Thanks & Regards,
Jack

--

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-------------------------------
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-------------------------------

[Hiram Clawson]

Good Morning Jack:

We discontinued use of mediawiki for login authentication in early 2012.
You can now use the built-in hgLogin function for login authentication:
http://genomewiki.ucsc.edu/index.php/Enabling_hgLogin

You must update all your data, not just hgcentral, any time you update
the software. The software and the data go together. You can use
the scripts in the source tree src/product/scripts/ to help with
your update.

--Hiram

[Hiram Clawson]

Good Morning Jack:

Depends upon how you placed them in the system.
Do not use --delete with your rsync for the MySQL
databases. That would remove your tables.

Your additional tables should be in a secondary trackDb
table, not in the primary trackDb table. The MySQL update
will overwrite your primary trackDb table. See the notes
about this in the src/product/ex.hg.conf
You should review this ex.hg.conf to see if there are new
configuration items you can use that have been introduced
in the past two years.

--Hiram

On 2/18/14 2:12 AM, OW Jack Ling (GIS) wrote:
> Hi Hiram,
>

> Thanks !
>
> Will it affect those wiggle or bed permanent tracks that I've already loaded onto the mysql database ?

[OW Jack Ling (GIS)]

Hi Hiram,

Thanks !

Will it affect those wiggle or bed permanent tracks that I've already loaded onto the mysql database ?

Thanks & Regards,
Jack

-----Original Message-----
From: Hiram Clawson [mailto:hi...@soe.ucsc.edu]

Sent: Tuesday, 18 February, 2014 1:07 AM
To: OW Jack Ling (GIS); genome...@soe.ucsc.edu

[Hiram Clawson]

Yes, existing bed and wiggle tables will continue to work as they were.

--Hiram

On 2/19/14 5:21 PM, OW Jack Ling (GIS) wrote:
> Hi Hiram,
>

> Yes, additional tables are already in the secondary trackDb table and primary trackDb table only store standard UCSC Genome Browser data. I'm more worried of the bed and wiggle tables that was loaded previously using hgLoadBed and hgLoadWiggle as I've plenty of them. Will v295 still be able to read these tables without any problem ?

[Hiram Clawson]

Can you forward the information about your system:

$ uname -a
$ gcc -v

Do you know how you obtained the samtabix directory source ?

--Hiram

On 2/20/14 9:13 AM, Daofeng Li wrote:
> Hi Hiram,
>

> I have encountered a problem when building the v295 source. Any chance that
> you might have some suggestions about the problem? Thanks.
>
> $ make compile
>
> cd lib && make
>
> make[1]: Entering directory `/home/comp/twlab/dli/kent/src/hg/lib'
>
> make[1]: `../../lib/x86_64/jkhgap.a' is up to date.
>
> make[1]: Leaving directory `/home/comp/twlab/dli/kent/src/hg/lib'
>
> cd cartReset && echo cartReset && make compile
>
> cartReset
>
> make[1]: Entering directory `/home/comp/twlab/dli/kent/src/hg/cartReset'
>
> gcc -O -g -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE
> -DMACHTYPE_x86_64 -DUSE_SSL -DCOLOR32 -DUSE_SAMTABIX -DUSE_BAM -DUSE_TABIX
> -DKNETFILE_HOOKS -Wall -I../inc -I../../inc -I../../../inc
> -I../../../../inc -I../../../../../inc -I/include
> -I/home/comp/twlab/dli/samtabix -o cartReset.o -c cartReset.c
>
> gcc cartReset.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a
> -pthread -L/lib -lssl -lcrypto -lpng
> /home/comp/twlab/dli/samtabix/libsamtabix.a -lz -lm
> /srv/epg/data/dli/mysql/lib/mysql/libmysqlclient.a -lz -lstdc++ -lrt
>
> /home/comp/twlab/dli/samtabix/libsamtabix.a(knetfile.o): In function
> `socket_wait':
>
> /home/comp/twlab/dli/samtabix/knetfile.c:126: undefined reference to
> `__fdelt_chk'
>
> collect2: ld returned 1 exit status
>
> make[1]: *** [compile] Error 1
>
> make[1]: Leaving directory `/home/comp/twlab/dli/kent/src/hg/cartReset'
>
> make: *** [cartReset.compile] Error 2
>
> Daofeng

[OW Jack Ling (GIS)]

Hi Hiram,

Yes, additional tables are already in the secondary trackDb table and primary trackDb table only store standard UCSC Genome Browser data. I'm more worried of the bed and wiggle tables that was loaded previously using hgLoadBed and hgLoadWiggle as I've plenty of them. Will v295 still be able to read these tables without any problem ?

[Daofeng Li]

Hi Hiram,

I have encountered a problem when building the v295 source. Any chance that you might have some suggestions about the problem? Thanks.

$ make compile

cd lib && make

make[1]: Entering directory `/home/comp/twlab/dli/kent/src/hg/lib'

make[1]: `../../lib/x86_64/jkhgap.a' is up to date.

make[1]: Leaving directory `/home/comp/twlab/dli/kent/src/hg/lib'

cd cartReset && echo cartReset && make compile

cartReset

make[1]: Entering directory `/home/comp/twlab/dli/kent/src/hg/cartReset'

gcc -O -g  -Wall -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DUSE_SSL -DCOLOR32 -DUSE_SAMTABIX -DUSE_BAM -DUSE_TABIX -DKNETFILE_HOOKS   -Wall -I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I/include  -I/home/comp/twlab/dli/samtabix  -o cartReset.o -c cartReset.c

gcc cartReset.o ../../lib/x86_64/jkhgap.a ../../lib/x86_64/jkweb.a  -pthread -L/lib -lssl -lcrypto -lpng /home/comp/twlab/dli/samtabix/libsamtabix.a -lz -lm /srv/epg/data/dli/mysql/lib/mysql/libmysqlclient.a -lz -lstdc++ -lrt 

/home/comp/twlab/dli/samtabix/libsamtabix.a(knetfile.o): In function `socket_wait':

/home/comp/twlab/dli/samtabix/knetfile.c:126: undefined reference to `__fdelt_chk'

collect2: ld returned 1 exit status

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

make[1]: Leaving directory `/home/comp/twlab/dli/kent/src/hg/cartReset'

make: *** [cartReset.compile] Error 2

Daofeng

On Wed, Feb 12, 2014 at 2:41 PM, Hiram Clawson <hi...@soe.ucsc.edu> wrote:

--

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[Daofeng Li]

my bad, Hiram...so I had compiled samtabix library in another server as we have shared home file system.

I recompile samtabix and now I have no problems.

Thanks again.

Daofeng

On Thu, Feb 20, 2014 at 11:18 AM, Daofeng Li <lid...@gmail.com> wrote:

Thanks for fast response Hiram. I obtained samtabix through git just today, (in the wiki):

git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix
cd samtabix
make

Here are the version information:

dli@epg:~$ uname -a

Linux epg 3.0.0-16-server #28-Ubuntu SMP Fri Jan 27 18:03:45 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

dli@epg:~$ gcc -v

Using built-in specs.

COLLECT_GCC=gcc

COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6.1/lto-wrapper

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.1-9ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++,go --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu

Thread model: posix

gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3) 

Daofeng

email to genome-mirror+unsubscribe@soe.ucsc.edu.

--

To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirror+unsubscribe@soe.ucsc.edu.

[Daofeng Li]

Thanks for fast response Hiram. I obtained samtabix through git just today, (in the wiki):

git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix
cd samtabix
make

Here are the version information:

dli@epg:~$ uname -a

Linux epg 3.0.0-16-server #28-Ubuntu SMP Fri Jan 27 18:03:45 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

dli@epg:~$ gcc -v

Using built-in specs.

COLLECT_GCC=gcc

COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6.1/lto-wrapper

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.1-9ubuntu3' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++,go --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu

Thread model: posix

gcc version 4.6.1 (Ubuntu/Linaro 4.6.1-9ubuntu3) 

Daofeng

On Thu, Feb 20, 2014 at 11:16 AM, Hiram Clawson <hi...@soe.ucsc.edu> wrote:

email to genome-mirror+unsubscribe@soe.ucsc.edu.

--

To unsubscribe from this group and stop receiving emails from it, send an email to genome-mirror+unsubscribe@soe.ucsc.edu.

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v296 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v296.zip

The version v296 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v297 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:
http://hgdownload.soe.ucsc.edu/admin/jksrc.v296.zip

The version v297 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v298 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v298.zip

The version v298 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v299 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v299.zip

The version v299 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

Summaries of changes can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene

hgGenome hgHubConnect hgLiftOver hgLogin hgMirror hgNear hgPal hgPcr hgRenderTracks

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v300 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v300.zip

The version v300 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v301 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v301.zip

The version v301 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v302 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v302.zip

The version v3012 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

Summaries of changes can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene
hgGenome hgHubConnect hgLiftOver hgLogin hgMirror hgNear hgPal hgPcr hgRenderTracks
hgSession hgSuggest hgTables hgTrackUi hgTracks hgUserSuggestion hgVai
hgVisiGene hgc phyloGif


and these configuration files:

/usr/local/apache/cgi-bin/all.joiner

/usr/local/apache/cgi-bin/greatData/*
/usr/local/apache/cgi-bin/hgCgiData/*
/usr/local/apache/cgi-bin/hgGeneData/*
/usr/local/apache/cgi-bin/hgNearData/*
/usr/local/apache/cgi-bin/hgcData/*
/usr/local/apache/cgi-bin/loader/*
/usr/local/apache/cgi-bin/lsSnpPdbChimera.py
/usr/local/apache/cgi-bin/visiGeneData/*

Please rsync --delete these directories:

/usr/local/apache/htdocs/js/*
/usr/local/apache/htdocs/style/*

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v303 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v303.zip

The version v303 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v304 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v304.zip

The version v304 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v305 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v305.zip

The version v305 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v306 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v306.zip

The version v306 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v307 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v307.zip

The version v307 CGI binaries can be found at:

can be used to update your htdocs directory with the correct delete
operation on /js/ and /style/ directories.

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v308 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v308.zip

The version v308 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

****
NOTE: November 2014 - The genome browser system can now be obtained
**** in a Virtual Box VM image from the 'Genome Store':
https://genome-store.ucsc.edu/
See also: http://genome.ucsc.edu/goldenPath/help/gbib.html

Summaries of changes for this version update can be found here:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v310 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v310.zip

The version v310 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v311 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v311.zip

The version v311 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v312 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v312.zip

The version v312 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

****
NOTE: November 2014 - The genome browser system can now be obtained
**** in a Virtual Box VM image from the 'Genome Store':
https://genome-store.ucsc.edu/
See also: http://genome.ucsc.edu/goldenPath/help/gbib.html

Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene
hgGenome hgHubConnect hgLiftOver hgLogin hgMirror hgNear hgPal hgPcr
hgRenderTracks hgSession hgSuggest hgTables hgTrackUi hgTracks hgUserSuggestion

hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloGif

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v313 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v313.zip

The version v313 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v314 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v314.zip

The version v314 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v315 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v315.zip

The version v315 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

****

NOTE: The genome browser system can now be obtained in a Virtual Box VM
**** image from the 'Genome Store':

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v315 source is now available at:
http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v316.zip

[Hiram Clawson]

Correction: v316

The version v316 source is now available at:
http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v317 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v317.zip

The version v317 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

****
NOTE: The genome browser system can now be obtained in a Virtual Box VM
**** image from the 'Genome Store':
https://genome-store.ucsc.edu/
See also: http://genome.ucsc.edu/goldenPath/help/gbib.html

Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene

hgGenome hgHubConnect hgIntegrator hgLiftOver hgLogin hgMirror hgNear hgPal

hgPcr hgRenderTracks hgSession hgSuggest hgTables hgTrackUi hgTracks
hgUserSuggestion hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloGif

(note: new binary with recent releases: hgIntegrator)

and these configuration files:

/usr/local/apache/cgi-bin/all.joiner
/usr/local/apache/cgi-bin/greatData/*
/usr/local/apache/cgi-bin/hgCgiData/*
/usr/local/apache/cgi-bin/hgGeneData/*
/usr/local/apache/cgi-bin/hgNearData/*
/usr/local/apache/cgi-bin/hgcData/*
/usr/local/apache/cgi-bin/loader/*

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v318 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v318.zip

The version v318 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

****
NOTE: The genome browser system can now be obtained in a Virtual Box VM
**** image from the 'Genome Store':
https://genome-store.ucsc.edu/
See also: http://genome.ucsc.edu/goldenPath/help/gbib.html

Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene

hgGenome hgHubConnect hgIntegrator hgLiftOver hgLogin hgMenubar hgMirror hgNear

hgPal hgPcr hgRenderTracks hgSession hgSuggest hgTables hgTrackUi hgTracks
hgUserSuggestion hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloGif

(note: new binaries with release v317: hgIntegrator, release v318: hgMenubar)

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v319 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v319.zip

The version v319 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v320 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v320.zip

The version v320 CGI binaries can be found at:

[Hiram Clawson]

Good Morning Genome Browser Mirror Site Operators:

The version v321 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v321.zip

The version v321 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

*****

NOTE: The genome browser system can now be obtained in a Virtual Box VM

***** image from the 'Genome Store':

https://genome-store.ucsc.edu/
See also: http://genome.ucsc.edu/goldenPath/help/gbib.html

Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene
hgGenome hgHubConnect hgIntegrator hgLiftOver hgLogin hgMenubar hgMirror hgNear
hgPal hgPcr hgRenderTracks hgSession hgSuggest hgTables hgTrackUi hgTracks
hgUserSuggestion hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloGif

(note: new binaries with:

release v317: hgIntegrator June 2015,
release v318: hgMenubar June 2015)

[Hiram Clawson]

Good Evening Genome Browser Mirror Site Operators:

The version v322 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v322.zip

The version v322 CGI binaries can be found at:

[Hiram Clawson]

Good Afternoon Genome Browser Mirror Site Operators:

The version v323 source is now available at:

http://hgdownload.soe.ucsc.edu/admin/jksrc.zip

or labelled with source number:

http://hgdownload.soe.ucsc.edu/admin/jksrc.v323.zip

The version v323 CGI binaries can be found at:

rsync -avP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ ${WEBROOT}/cgi-bin/
or: ftp://hgdownload.cse.ucsc.edu/apache/cgi-bin/

A license is required for commercial download and/or installation of
the Genome Browser binaries and source code. No license is needed for
academic, nonprofit, and personal use.

*****
NOTE: The genome browser system can now be obtained in a Virtual Box VM
***** image from the 'Genome Store':
https://genome-store.ucsc.edu/
See also: http://genome.ucsc.edu/goldenPath/help/gbib.html

Summaries of changes for this version update can be found here:
http://genecats.soe.ucsc.edu/builds/versions.html

The following CGIs were updated:

cartDump cartReset das hgApi hgBlat hgConvert hgCustom hgEncodeApi
hgEncodeDataVersions hgEncodeVocab hgFileSearch hgFileUi hgGateway hgGene
hgGenome hgHubConnect hgIntegrator hgLiftOver hgLogin hgMenubar hgMirror hgNear
hgPal hgPcr hgRenderTracks hgSession hgSuggest hgTables hgTrackUi hgTracks
hgUserSuggestion hgVai hgVisiGene hgc lsSnpPdbChimera.py phyloGif

(note: new binaries with:
release v317: hgIntegrator June 2015,
release v318: hgMenubar June 2015)

and these configuration files:

/usr/local/apache/cgi-bin/all.joiner

/usr/local/apache/cgi-bin/extTools.ra

/usr/local/apache/cgi-bin/greatData/*
/usr/local/apache/cgi-bin/hgCgiData/*
/usr/local/apache/cgi-bin/hgGeneData/*
/usr/local/apache/cgi-bin/hgNearData/*
/usr/local/apache/cgi-bin/hgcData/*
/usr/local/apache/cgi-bin/loader/*
/usr/local/apache/cgi-bin/visiGeneData/*

(note: new configuration file: release v323: extTools.ra October 2015)