I was successful in getting the bps_python egg to load finally.  However,
there is an issue that remains.  When I submit a job it is sent to the
local runner and not to pbs.  Where should I start looking to change this
work?  

Thanks,
Iry

On 7/10/12 12:00 PM, "galaxy-dev-requ...@lists.bx.psu.edu"
<galaxy-dev-requ...@lists.bx.psu.edu> wrote:

>
>Message: 3
>Date: Mon, 9 Jul 2012 17:24:25 +0000
>From: Iry Witham <iry.wit...@jax.org>
>To: "Dorset, Daniel C" <daniel.dor...@vanderbilt.edu>
>Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10
>Message-ID: <cc207dde.8f49%iry.wit...@jax.org>
>Content-Type: text/plain; charset="us-ascii"
>
>Hi Daniel,
>
>       I did use -e previously.  The ?e was a typo in my post.  I ran it again
>and it tries, but fails to generate the file(s) as shown:
>
>:galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist>
>LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
>fetch_one(): Trying to fetch:
>  http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz
>fetch_one(): Fetched to:
>  
>/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/archives/pbs
>_
>python-4.1.0.tar.gz
>unpack_source(): Unpacked to:
>  
>/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-
>l
>inux-x86_64-ucs4/pbs_python
>copy_build_script(): Using build script
>/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/scripts/pbs_
>p
>ython.py
>run_scramble_script(): Beginning build
>run_scramble_script(): Executing in
>/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-
>l
>inux-x86_64-ucs4/pbs_python:
>  /usr/bin/python scramble.py
>
>--------------------------------------------------------------------------
>-
>This script requires setuptools version 0.6c11 to run (even to display
>help).  I will attempt to download it for you (from
>http://pypi.python.org/packages/2.6/s/setuptools/), but
>you may need to enable firewall access for this script first.
>I will start the download in 8 seconds.
>
>(Note: if this machine does not have network access, please obtain the
>file
>
>   
>http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e
>g
>g
>
>and place it in this directory before rerunning this script.)
>--------------------------------------------------------------------------
>-
>Downloading 
>http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e
>g
>g
>checking for pbs-config... /usr/local/lib//../bin/pbs-config
>Found torque version: 2.5.8
>checking for python... /usr/bin/python
>checking for python version... 2.6
>checking for python platform... linux2
>checking for python script directory...
>${prefix}/lib64/python2.6/site-packages
>checking for python extension module directory...
>${exec_prefix}/lib64/python2.6/site-packages
>configure: creating ./config.status
>config.status: creating Makefile
>config.status: creating setup.py
>scramble(): Patching setup.py
>running egg_info
>creating src/pbs_python.egg-info
>writing src/pbs_python.egg-info/PKG-INFO
>writing top-level names to src/pbs_python.egg-info/top_level.txt
>writing dependency_links to src/pbs_python.egg-info/dependency_links.txt
>writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
>reading manifest file 'src/pbs_python.egg-info/SOURCES.txt'
>writing manifest file 'src/pbs_python.egg-info/SOURCES.txt'
>running bdist_egg
>installing library code to build/bdist.linux-x86_64/egg
>running install_lib
>running build_py
>creating build
>creating build/lib.linux-x86_64-2.6
>copying src/pbs.py -> build/lib.linux-x86_64-2.6
>copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6
>running build_ext
>building '_pbs' extension
>creating build/temp.linux-x86_64-2.6
>creating build/temp.linux-x86_64-2.6/src
>gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall
>-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
>-fasynchronous-unwind-tables -g -fwrapv -fPIC -DTORQUE_2_4
>-I/usr/include/python2.6 -c src/pbs_wrap.c -o
>build/temp.linux-x86_64-2.6/src/pbs_wrap.o
>gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o
>-L/usr/local/lib -L/usr/lib64 -ltorque -lpython2.6 -o
>build/lib.linux-x86_64-2.6/_pbs.so
>creating build/bdist.linux-x86_64
>creating build/bdist.linux-x86_64/egg
>copying build/lib.linux-x86_64-2.6/PBSQuery.py ->
>build/bdist.linux-x86_64/egg
>copying build/lib.linux-x86_64-2.6/pbs.py -> build/bdist.linux-x86_64/egg
>copying build/lib.linux-x86_64-2.6/_pbs.so -> build/bdist.linux-x86_64/egg
>byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc
>byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc
>creating stub loader for _pbs.so
>byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc
>creating build/bdist.linux-x86_64/egg/EGG-INFO
>copying src/pbs_python.egg-info/PKG-INFO ->
>build/bdist.linux-x86_64/egg/EGG-INFO
>copying src/pbs_python.egg-info/SOURCES.txt ->
>build/bdist.linux-x86_64/egg/EGG-INFO
>copying src/pbs_python.egg-info/dependency_links.txt ->
>build/bdist.linux-x86_64/egg/EGG-INFO
>copying src/pbs_python.egg-info/top_level.txt ->
>build/bdist.linux-x86_64/egg/EGG-INFO
>writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt
>zip_safe flag not set; analyzing archive contents...
>creating dist
>creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg' and adding
>'build/bdist.linux-x86_64/egg' to it
>removing 'build/bdist.linux-x86_64/egg' (and everything under it)
>Traceback (most recent call last):
>  File "scripts/scramble.py", line 50, in <module>
>    egg.scramble()
>  File 
>"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/scramble.py"
>,
> line 60, in scramble
>    raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to
>fail, but no egg found to copy from expected path:\n  %s" % (
>sys._getframe().f_code.co_name, self.name, new_egg ) )
>galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python
>did not appear to fail, but no egg found to copy from expected path:
>  
>/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6-
>l
>inux-x86_64-ucs4/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.
>e
>gg"
>
>Iry
>
>On 7/7/12 3:10 PM, "Dorset, Daniel C" <daniel.dor...@vanderbilt.edu>
>wrote:
>
>>
>>________________________________________
>>From: galaxy-dev-boun...@lists.bx.psu.edu
>>[galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of
>>galaxy-dev-requ...@lists.bx.psu.edu [galaxy-dev-requ...@lists.bx.psu.edu]
>>Sent: Saturday, July 07, 2012 11:00 AM
>>To: galaxy-dev@lists.bx.psu.edu
>>Subject: galaxy-dev Digest, Vol 73, Issue 10
>>
>>Send galaxy-dev mailing list submissions to
>>        galaxy-dev@lists.bx.psu.edu
>>
>>To subscribe or unsubscribe via the World Wide Web, visit
>>        http://lists.bx.psu.edu/listinfo/galaxy-dev
>>or, via email, send a message with subject or body 'help' to
>>        galaxy-dev-requ...@lists.bx.psu.edu
>>
>>You can reach the person managing the list at
>>        galaxy-dev-ow...@lists.bx.psu.edu
>>
>>When replying, please edit your Subject line so it is more specific
>>than "Re: Contents of galaxy-dev digest..."
>>
>>
>>HEY!  This is important!  If you reply to a thread in a digest, please
>>1. Change the subject of your response from "Galaxy-dev Digest Vol ..."
>>to the original subject for the thread.
>>2. Strip out everything else in the digest that is not part of the thread
>>you are responding to.
>>
>>Why?
>>1. This will keep the subject meaningful.  People will have some idea
>>from the subject line if they should read it or not.
>>2. Not doing this greatly increases the number of emails that match
>>search queries, but that aren't actually informative.
>>
>>Today's Topics:
>>
>>   1. pbs_python issues (Iry Witham)
>>   2. Which css file does welcome.html use? (Dorset, Daniel C)
>>   3. Re: Which css file does welcome.html use? (Jeremy Goecks)
>>
>>
>>Hi Ira,
>>
>>I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster,
>>and I went through this process a couple of months ago. If I remember
>>correctly, when you run your Python script, you're supposed to run it
>>with "-e" not "?e" Assuming that you are pointing to the correct
>>directory, it looks like everything else about your command is correct.
>>
>>Have you tried that?
>>
>>----------------------------------------------------------------------
>>
>>Message: 1
>>Date: Fri, 6 Jul 2012 16:32:14 +0000
>>From: Iry Witham <iry.wit...@jax.org>
>>To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>>Subject: [galaxy-dev] pbs_python issues
>>Message-ID: <cc1c8b4d.8ead%iry.wit...@jax.org>
>>Content-Type: text/plain; charset="windows-1252"
>>
>>I am having an issue with pbs_python loading, but not submitting jobs to
>>the cluster.
>>
>>The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python
>>scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python
>>egg in the /galaxy-dist/eggs/ directory.
>>
>>Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from
>>my production galaxy server and restarted my test server.  It appears to
>>start, but when I attempt to run anything it uses the local runner and
>>fails.  The runner0.log shows the pbsjobrunner is loaded is below:
>>
>>galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner:
>>galaxy.jobs.runners.pbs:PBSJobRunner
>>galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue
>>started
>>galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue
>>started
>>galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue
>>started
>>galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue
>>started
>>
>>I can't seem to get past this point since I upgraded.  Can someone point
>>me in the right direction?
>>
>>Thanks,
>>Iry
>>
>>
>>The information in this email, including attachments, may be confidential
>>and is intended solely for the addressee(s). If you believe you received
>>this email by mistake, please notify the sender by return email as soon
>>as possible.
>>-------------- next part --------------
>>An HTML attachment was scrubbed...
>>URL: 
>><http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120706/a179a8
>>0
>>8/attachment-0001.html>
>>
>>------------------------------
>>
>>Message: 2
>>Date: Fri, 6 Jul 2012 16:28:08 -0500
>>From: "Dorset, Daniel C" <daniel.dor...@vanderbilt.edu>
>>To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>>Subject: [galaxy-dev] Which css file does welcome.html use?
>>Message-ID:
>>        
>><9b568b41976b54469cc6e3fd758ef83105dc006...@its-drwnem10.ds.vanderbilt.ed
>>u
>>>
>>
>>Content-Type: text/plain; charset="us-ascii"
>>
>>OK, this is ostensibly a simple question. However, I can't find the CSS
>>file that welcome.html is using. In the HTML file, there's this line:
>>
>><link rel="stylesheet" href="style/base.css" type="text/css" />
>>
>>However, I don't see a directory named "style" anywhere in the galaxy
>>directory tree. When I search for "base.css," from the root Galaxy
>>installation directory, I get the following results:
>>
>>./static/june_2007_style/blue/base.css
>>./static/light_hatched_style/blue/base.css
>>./static/light_hatched_style/green/base.css
>>./static/old_blue_style/base.css
>>
>>So I assume that one of these is being used? I do think it's strange
>>though, that the HTML points to an apparently non-existent file and yet
>>everything on my local instance looks identical to the Penn State Public
>>site.
>>
>>Thanks,
>>
>>Dan
>>-------------- next part --------------
>>An HTML attachment was scrubbed...
>>URL: 
>><http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20120706/af3796
>>a
>>9/attachment-0001.html>
>>
>>------------------------------
>>
>>Message: 3
>>Date: Fri, 6 Jul 2012 18:12:41 -0400
>>From: Jeremy Goecks <jeremy.goe...@emory.edu>
>>To: "Dorset, Daniel C" <daniel.dor...@vanderbilt.edu>
>>Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
>>Subject: Re: [galaxy-dev] Which css file does welcome.html use?
>>Message-ID: <d1013340-bd6c-475f-bd9d-979746db3...@emory.edu>
>>Content-Type: text/plain; charset="windows-1252"
>>
>>The CSS files used by Galaxy, including base.css, are under
>>./static/june_2007_style/blue . There is a route used to point to the
>>correct location for CSS data.
>>
>>Best,
>>J.
>>
>>On Jul 6, 2012, at 5:28 PM, Dorset, Daniel C wrote:
>>
>>> OK, this is ostensibly a simple question. However, I can?t find the CSS
>>>file that welcome.html is using. In the HTML file, there?s this line:
>>>
>>> <link rel="stylesheet" href="style/base.css" type="text/css" />
>>>
>>> However, I don?t see a directory named ?style? anywhere in the galaxy
>>>directory tree. When I search for ?base.css,? from the root Galaxy
>>>installation directory, I get the following results:
>>>
>>> ./static/june_2007_style/blue/base.css
>>> ./static/light_hatched_style/blue/base.css
>>> ./static/light_hatched_style/green/base.css
>>> ./static/old_blue_style/base.css
>>>
>>> So I assume that one of these is being used? I do think it?s strange
>>>though, that the HTML points to an apparently non-existent file and yet
>>>everything on my local instance looks identical to the Penn State Public
>>>site.
>>>
>>> Thanks,
>>>
>>> Dan
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>
>>>  http://lists.bx.psu.edu/
>>
>>-------------- next part --------------
>>An HTML attachment was scrubbed...
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>>e/attachment-0001.html>
>>
>>------------------------------
>>
>>_______________________________________________
>>galaxy-dev mailing list
>>galaxy-dev@lists.bx.psu.edu
>>http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>>
>>End of galaxy-dev Digest, Vol 73, Issue 10
>>******************************************
>>
>>
>
>
>The information in this email, including attachments, may be confidential
>and is intended solely for the addressee(s). If you believe you received
>this email by mistake, please notify the sender by return email as soon
>as possible.
>
>
>
>------------------------------
>
>Message: 4
>Date: Mon, 9 Jul 2012 11:24:57 -0600
>From: Luobin Yang <yangl...@isu.edu>
>To: Greg Von Kuster <g...@bx.psu.edu>
>Cc: "galaxy-...@bx.psu.edu" <galaxy-...@bx.psu.edu>, "TerAvest,        Emily"
>       <emily.terav...@codexis.com>
>Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in
>       queue"  forever
>Message-ID:
>       <CAOWbOwAhR3JPOgRpKabkbRgt5UQD=XnQLdW=mkziw2rue8e...@mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Hi, Greg,
>
>I've still got issues after I downloaded the latest version from the dist
>repository. So after I selected the datasets that I would like to transfer
>from the sequencer and click the "Transfer" button, Galaxy generates an
>error message : "Invalid sample id (None)"... I tried to delete this
>dataset using the "manage datasets" menu, and Galaxy generates the same
>error message: "Invalid sample id (None)". It seems galaxy system
>generates
>the sample id automatically (the first one is sample_1), not sure why this
>happens...
>
>Luobin
>
>
>On Fri, Mar 30, 2012 at 8:30 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>
>> Hello Emily,
>>
>> This issue should be resolved in change set 6924:12b14f3e78e9, which is
>> currently only available from our central repository.  It will not be
>> available in the dist repository fro some time, so you'll have to pull
>>it
>> from Galaxy central (https://bitbucket.org/galaxy/galaxy-central) if you
>> want it now.
>>
>> Thanks very much for reporting this problem, and we apologize for the
>> inconvenience it caused.
>>
>> Greg Von Kuster
>>
>>
>> On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote:
>>
>> >
>> > Hi Leandro,
>> >
>> > I am also experiencing the same problem with the latest version of
>> galaxy. I just attempted to connect our sequencer for the first time
>> yesterday. I do not have an older version of galaxy to test and compare
>>to
>> see if it works in earlier versions. I am able to transfer data from the
>> sequence to the import directory, however it is not moved to the data
>> library. My data_transfer.log also has the same error.
>> > "The server could not comply with the request since it is either
>> malformed or otherwise incorrect."
>> >
>> > Does anyone have a solution for this?
>> >
>> > Thanks
>> > Emily
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 17
>> > Date: Wed, 28 Mar 2012 13:15:47 +0200
>> > From: Leandro Hermida <soft...@leandrohermida.com>
>> > To: Luobin Yang <yangl...@isu.edu>
>> > Cc: Galaxy Dev <galaxy-...@bx.psu.edu>
>> > Subject: Re: [galaxy-dev] Sample tracking data transfer hangs "in
>> >       queue"  forever
>> > Message-ID:
>> >       <
>> caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek...@mail.gmail.com>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > Dear Galaxy Dev,
>> >
>> > Ok I have gotten further found out what was going on, in my
>> > data_transfer.log I was getting HTTP 404 Not Authorized when the data
>> > transfer was trying to access Galaxy API URLs
>> > http://galaxyserver/api/... This is because we are using external user
>> > authentication as documented in
>> > http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy and this puts
>> > all of Galaxy behind this authentication. Since the Galaxy API uses
>> > API keys to essentially authenticate you have to change you <Location
>> > /> ... </Location> container to not match URLs starting with /api. To
>> > do this you have to change it to <LocationMatch "^/(?!api)"> ....
>> > </LocationMatch>.
>> >
>> > best,
>> > leandro
>> >
>> > On Mon, Mar 26, 2012 at 6:10 PM, Luobin Yang <yangl...@isu.edu> wrote:
>> >> I've got the same problem and when I looked at the
>>data_transfer.log, I
>> saw
>> >> the following message:
>> >>
>> >> 2012-03-01 15:12:27,338 - datatx_13870 -
>> >> (u'9c17d84742cd2acb63d88b5bd41d968f',
>> >> u'http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
>> >> {'sample_dataset_ids': ['a799d38679e985db', '33b43b4e7093c91f'],
>> >> 'error_msg': '', 'update_type': 'sample_dataset_transfer_status',
>> >> 'new_status': 'Adding to data library'})
>> >> 2012-03-01 15:12:27,342 - datatx_13870 - Error. <!DOCTYPE HTML PUBLIC
>> >> "-//IETF//DTD HTML 2.0//EN">
>> >> <html><head>
>> >> <title>405 Method Not Allowed</title>
>> >> </head><body>
>> >> <h1>Method Not Allowed</h1>
>> >> <p>The requested method PUT is not allowed for the URL
>> >> /api/samples/2d9035b3fc152403.</p>
>> >> <hr>
>> >>
>> >> Using Galaxy instead of Apache as the web server changed the sample
>> status
>> >> from "in queue" to complete but didn't add the downloaded files to
>>the
>> data
>> >> library.
>> >>
>> >> Luobin
>> >>
>> >> On Mon, Mar 26, 2012 at 9:54 AM, Leandro Hermida
>> >> <soft...@leandrohermida.com> wrote:
>> >>>
>> >>> Dear Galaxy Dev,
>> >>>
>> >>> I've set up the Galaxy sample tracking system data transfer
>> >>> functionality exactly as specified here
>> >>> https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I
>> >>> attempt to transfer datasets it puts them into the queue and then
>> >>> never seems to transfer anything.
>> >>>
>> >>> The galaxy_listener.log shows:
>> >>>
>> >>> 2012-03-26 17:16:24,515 - GalaxyAMQP - GALAXY LISTENER PID: 8738 -
>> >>> {'config_file': 'universe_wsgi.ini', 'http_server_section':
>> >>> 'server:main'}
>> >>> 2012-03-26 17:16:24,518 - GalaxyAMQP - {'exchange':
>>'galaxy_exchange',
>> >>> 'rabbitmqctl_path':
>> >>>
>> >>>
>> 
>>'/gpfshpc/software/pmrdcdb/galaxy/rabbitmq/rabbitmq_server-2.8.1/sbin/rab
>>bitmqctl',
>> >>> 'userid': 'galaxy_dev', 'routing_key': 'bar_code_scanner', 'queue':
>> >>> 'galaxy_queue', 'host': '127.0.0.1', 'virtual_host':
>> >>> 'galaxy_dev_messaging_engine', 'password': 'mypassword', 'port':
>> >>> '5672'}
>> >>> 2012-03-26 17:16:24,565 - GalaxyAMQP - Connected to rabbitmq server
>>-
>> >>> 127.0.0.1:5672
>> >>> 2012-03-26 17:31:23,393 - GalaxyAMQP - MESSAGE RECVD: data_transfer
>> >>> 2012-03-26 17:31:23,393 - GalaxyAMQP - DATA TRANSFER
>> >>> 2012-03-26 17:31:23,401 - GalaxyAMQP - Started process (25406):
>>python
>> >>>
>> >>>
>> 
>>"/gpfshpc/software/pmrdcdb/galaxy/galaxy_dist_dev/scripts/galaxy_messagin
>>g/server/data_transfer.py"
>> >>> " <data_transfer>
>> >>> <galaxy_host>rd-galaxydev.app.pmi</galaxy_host>
>> >>> <api_key>69bbd1a9b18eda2a888e9963820d8ef0</api_key>
>> >>> <data_host>chp723</data_host>
>> >>> <data_user>galaxy</data_user>
>> >>> <data_password>mypassword</data_password>
>> >>> <request_id>12</request_id>
>> >>> <sample_id>12</sample_id>
>> >>> <library_id>15</library_id>
>> >>> <folder_id>52</folder_id> ? ? ? ? ? ? ? ? ? ?<dataset>
>> >>> ?<dataset_id>10</dataset_id>
>> >>> <name>ttt_2.fastq.gz</name>
>> >>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-2.fastq.gz</file>
>> >>> ? ? ? ? ?</dataset><dataset>
>> >>> <dataset_id>9</dataset_id>
>> >>> <name>ttt_1.fastq.gz</name>
>> >>> <file>/gpfshpc/data/pmrdcdb/RNA-Seq/datasets/ttt-1.fastq.gz</file>
>> >>> ? ? ? ? ?</dataset> ? ? ? ? ? ? ? ?</data_transfer>"
>> >>> "universe_wsgi.ini"
>> >>>
>> >>> The FASTQ files are for testing and aren't very big (7.6 MB), what
>> >>> could be going wrong?
>> >>>
>> >>> regards,
>> >>> Leandro
>> >>> ___________________________________________________________
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>> >>
>> >>
>> >
>> >
>> > ************
>> > This email message and any electronic files transmitted with it
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>> to the official business of Codexis, Inc. and its
>> > affiliates are proprietary, strictly confidential, and may be legally
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>>
>> ___________________________________________________________
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>>
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>>
>-------------- next part --------------
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>------------------------------
>
>Message: 5
>Date: Mon, 9 Jul 2012 11:09:24 -0700
>From: Dave Lin <d...@verdematics.com>
>To: Galaxy-dev <galaxy-dev@lists.bx.psu.edu>
>Subject: [galaxy-dev] Automating customized setup of cloudman galaxy
>Message-ID:
>       <CADnw0gN==E4fVem8oUy_=bnf3o-wndeee9e_uw3dn9dssjt...@mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Dear Galaxy Dev Team-
>
>I'm looking to automate the complete setup/build of a customized galaxy
>cluster from the command line.
>I'm looking for help/suggestions on several steps (labeled MANUAL) where
>it
>currently requires manual ui-input
>
>
>1) [Automated] Have a script that uses cloudman + ec2-api-tools to create
>new galaxy cluster on Amazon from scratch.
>
>2) [MANUAL] open browser to the new instance, enter volume size and start
>a
>new cluster. (Looking to be invoke this via command-line)
>
>3) [MANUAL] Create standard users via the galaxy ui.  (looking to be able
>to create a few standard users via command-line, not UI)
>
>4) [MANUAL] Update galaxy to galaxy-dev tip using the galaxy-ui.  (Can I
>just run hg pull/update? There doesn't seem to be the mercurial metadata
>in
>the galaxy-central directory.)
>
>5) [Automated] Pull custom code from personal bitbucket, apply changes,
>create missing directories, install tools, etc. Copy over various configs
>(toos_conf.xml , universe_wsgi,etc)
>
>6)  [MANUAL] Import each workflow using the galaxy UI. (Have several
>workflows, and currently have to manually import them via the UI. I'm
>looking to make some type of command-line/api call that can pass the
>workflow to galaxy)
>
>
>I could go into the code and figure out how to call these functions or
>possibly just insert rows into the database. However, I'm looking to
>approach this using more official/supported API's.
>
>Would be happy to try to contribute/document this process once I have it
>working if others are interested.
>
>Thanks in advance,
>Dave
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>------------------------------
>
>Message: 6
>Date: Mon, 9 Jul 2012 15:55:12 -0500
>From: "Moore, Raymond M." <moore.raym...@mayo.edu>
>To: Peter Cock <p.j.a.c...@googlemail.com>
>Cc: Galaxy Dev <galaxy-...@bx.psu.edu>
>Subject: Re: [galaxy-dev] Ability to Select SGE queue?
>Message-ID:
>       <fa61f0f924eef542967b7874e9f1b4034a0...@msgebe14.mfad.mfroot.org>
>Content-Type: text/plain; charset="us-ascii"
>
>Thank you Peter,
>
>That's exactly what I was looking for. I'd really like to implement
>the functionality defined by John Chilton.
>
>The ability to select a queue based on the input size is very important
>to our group.
>
>Thanks again.
>
>-----Original Message-----
>From: Peter Cock [mailto:p.j.a.c...@googlemail.com]
>Sent: Monday, July 09, 2012 12:07 PM
>To: Moore, Raymond M.
>Cc: Galaxy Dev
>Subject: Re: [galaxy-dev] Ability to Select SGE queue?
>
>On Mon, Jul 9, 2012 at 5:34 PM, Moore, Raymond M.
><moore.raym...@mayo.edu> wrote:
>> I'd like to provide a choice to my users which size Queue they would
>> like to use when they are about to run a tool.
>>
>>   I'm using the SGE configuration through DRMAA on my local install.
>> I've only seen the queue set in the wsgi.ini file.
>>
>> Is there a way I can include this choice of SGE queue in my xml?
>>
>> Thanks
>
>You can set the queue for each tool in the universe.xml file, but that
>is all at the moment AFAIK.
>
>More flexible options currently requires modification to Galaxy, e.g.
>http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html
>
>Peter
>
>
>
>------------------------------
>
>Message: 7
>Date: Tue, 10 Jul 2012 08:43:58 +0200
>From: "Sascha Kastens" <s.kast...@gatc-biotech.com>
>To: <galaxy-...@bx.psu.edu>
>Subject: Re: [galaxy-dev] Job output not returned from Cluster
>Message-ID: <1780559704721497921508@SRV32>
>Content-Type: text/plain; charset="windows-1252"
>
>Hi Hemant,
>
>?
>
>thanks for your help. I have set the value to 100, but this did not fix
>the problem.
>
>I am now trying to get a NFS mounted with -noac.
>
>?
>
>Cheers,
>
>Sascha
>
>?
>
>Original Message
>
>processed by CONSOLIDATE
>
>Subject:
>
>RE: [galaxy-dev] Job output not returned from Cluster
>
>Sent:
>
>Montag, 9. Juli 2012 17:38
>
>From:
>
>Kelkar, Hemant (hkel...@unc.edu)
>
>
>Hi Sascha,
>
>?
>
>I am not sure if the error you are seeing is like one I had posted in
>this thread? 
>http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-faile
>d-quot-td4627406.html#a4632168
>
>?
>
>--Hemant
>
>?
>
>From: galaxy-dev-boun...@lists.bx.psu.edu
>[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Sascha Kastens
>Sent: Monday, July 09, 2012 11:26 AM
>To: galaxy-dev@lists.bx.psu.edu
>Subject: Re: [galaxy-dev] Job output not returned from Cluster
>
>?
>
>Hi!
>
>?
>
>Unfortunately I was not able to fix this problem yet.
>
>?
>
>Is anybody out there who had a similar problem while using Galaxy with
>SGE or has the knowledge about the things I can look at?
>
>?
>
>Thanks in advance!
>
>?
>
>Cheers,
>
>Sascha
>
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>http://lists.bx.psu.edu/listinfo/galaxy-dev
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>
>End of galaxy-dev Digest, Vol 73, Issue 13
>******************************************


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