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.eg
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.eg
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
>
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>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
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>------------------------------
>
>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.edu
>>
>
>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
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>------------------------------
>
>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/
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