February 2011 - galaxy-dev - lists.galaxyproject.org

maximum value for local_job_queue_workers
by hari krishna 25 Feb '11

25 Feb '11

Hi, What is the difference between threadpool_workers and local_job_queue_workers*.* what is the maximum size that i can set local_job_queue_workers value? -- Thanks & Regards, Hari Krishna .M

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Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster
by Nate Coraor 25 Feb '11

25 Feb '11

Hi Sonali, Since this is a local installation question, I have moved the discussion to galaxy-dev. Further responses are inline below. Sonali Amonkar wrote: > Hi, > > First of all I would like to appreciate the clean and neat documentation written for the Galaxy setup for Cluster. > > I am attempting to install Galaxy on Penguin cluster with Torque PBS manager. > While following the steps I came across an error as below: > > =========================================================================================================================================================== > [user@server pbs_python]$ /galaxy/Python-2.4.6/python scramble.py > > --------------------------------------------------------------------------- > This script requires setuptools version 0.6c12 to run (even to display > help). I will attempt to download it for you (from > http://pypi.python.org/packages/2.4/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/2.4/s/setuptools/setuptools-0.6c12-py2.4.egg > > and place it in this directory before rerunning this script.) > --------------------------------------------------------------------------- > Downloading http://pypi.python.org/packages/2.4/s/setuptools/setuptools-0.6c12-py2.4.egg > Traceback (most recent call last): > File "scramble.py", line 14, in ? > from scramble_lib import * > File "../../../lib/scramble_lib.py", line 150, in ? > use_setuptools( download_delay=8, to_dir=os.path.dirname( __file__ ) ) > File "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py", line 92, in use_setuptools > return do_download() > File "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py", line 70, in do_download > egg = download_setuptools(version, download_base, to_dir, download_delay) > File "/galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py", line 131, in download_setuptools > src = urllib2.urlopen(url) > File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 130, in urlopen > return _opener.open(url, data) > File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 364, in open > response = meth(req, response) > File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 471, in http_response > response = self.parent.error( > File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 402, in error > return self._call_chain(*args) > File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 337, in _call_chain > result = func(*args) > File "/galaxy/Python-2.4.6/Lib/urllib2.py", line 480, in http_error_default > raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) > urllib2.HTTPError: HTTP Error 404: Not Found > =========================================================================================================================================================== > > > The scramble script here is trying to download an egg which does not exist at the location (try opening the link it is trying to download in a browser - you'll get 404, then see the parent directory - http://pypi.python.org/packages/2.4/s/setuptools/ you'll see last version available i.e. 0.6c11). > Hi Sonali, 0.6c12 is still in development and I'm not sure where this is coming from. The version of ez_setup.py in: /galaxy/galaxy-dist/scripts/scramble/lib/ references 0.6c11, and this file is copied to the build directory in: galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ What's the value of DEFAULT_VERSION in: /galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/ez_setup.py ? > If we try to download the last version of setuptools 0.6c11 and rename it to the latest version (desperate attempt to make it work), that doesn't work either. > > =========================================================================================================================================================== > [user@server pbs_python]$ mv setuptools-0.6c11-py2.4.egg setuptools-0.6c12-py2.4.egg > > [user@server pbs_python]$ /galaxy/Python-2.4.6/python scramble.py > checking for pbs-config... /usr/lib64/../bin/pbs-config > Found torque version: 2.4.0-snap.200812091621 > checking for python... /galaxy/Python-2.4.6/python > checking for python version... 2.4 > checking for python platform... linux2 > checking for python script directory... ${prefix}/lib/python2.4/site-packages > checking for python extension module directory... ${exec_prefix}/lib/python2.4/site-packages > configure: creating ./config.status > config.status: creating Makefile > config.status: creating setup.py > scramble(): Patching setup.py > Traceback (most recent call last): > File "scramble.py", line 49, in ? > execfile( "setup.py", globals(), locals() ) > File "setup.py", line 32, in ? > build_version = int(tmp[2]) > ValueError: invalid literal for int(): 0-snap > > =========================================================================================================================================================== This is a problem with your TORQUE version and pbs_python's assumptions about its version numbering. pbs_python expects it to be all-numeric whereas yours is a development snapshot with a non-integer value in the revision portion of the version (2.4.0-snap.200812091621). ^^^^^^^^^^^^^^^^^^^ There are a few ways to proceed. One would be to upgrade your TORQUE client to a release version. Another would be to try the drmaa job runner instead of pbs, since TORQUE provides a DRMAA C library, although I don't believe anyone has used it with TORQUE yet. The last would be to modify pbs_python's build process. Start by changing directories to: /galaxy/galaxy-dist/scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python Edit setup.py and comment all of the following: #VERSION = "2.4.0-snap.200812091621" #tmp = VERSION.split('.') #major_version = int(tmp[0]) #minor_version = int(tmp[1]) #build_version = int(tmp[2]) #if major_version >= 2 and minor_version >= 4 and build_version >= 7: # os.symlink('pbs_wrap_2.4.c', 'pbs_wrap.c') # os.symlink('pbs_2.4.py', 'pbs.py') # TORQUE_VERSION='TORQUE_2_4' #else: And then force the old version by un-indenting or doing something silly like: if True: os.symlink('pbs_wrap_2.1.c', 'pbs_wrap.c') os.symlink('pbs_2.1.py', 'pbs.py') TORQUE_VERSION='TORQUE_OLD' However, running scramble.py again will overwrite your changes, so you will also need to modify scramble.py (in the same directory, not the main scramble.py in /galaxy/galaxy-dist/scripts) and comment out: #run( 'sh configure --with-pbsdir=%s' % os.environ['LIBTORQUE_DIR'], os.getcwd(), 'Running pbs_python configure script' ) Once this is done you should be able to run the *LOCAL* scramble.py in the build directory: $ /galaxy/Python-2.4.6/python ./scramble.py If this succeeds, the egg will be built and placed in the dist/ subdirectory. The egg can then be copied to: /galaxy/galaxy-dist/eggs/ Please let us know how this goes. --nate > > Do let me know if anyone else has faced this issue of the scramble script trying to download a wrong version? Greatly appreciate your time. > > Warm Regards, > Sonali Amonkar > > > > DISCLAIMER > ========== > This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user

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BOSC 2011 topic organizers and Codefest
by Brad Chapman 25 Feb '11

25 Feb '11

Hi all; This year the Bioinformatics Open Source Conference (BOSC) will be taking place in Vienna, Austria on July 15-16th. This is a yearly opportunity for open source bioinformatics developers to get together in person and discuss on-going projects. Nomi Harris, Peter Rice and the other organizing committee members are already hard at work planning for the conference: http://www.open-bio.org/wiki/BOSC_2011 The call for abstracts opens next Monday, and extends through April 18th, and we've been brainstorming potential session topics. This year we've tried to focus each of the sessions around a particular biological problem or computational approach. We hope this will draw some interesting parallels between work being done in different groups, and encourage even more collaboration. We are actively looking for community members who are interested in heading up the organization of a topic. The general idea is to build a cohesive set of talks within a session. How you'd like to do this is completely flexible but some of the ideas we've been discussing are: - Having a short introductory talk to provide an overview of an area, framing the different talks within this context. - Forgoing individual question/answer and instead combining this time into a longer panel-style discussion with all of the speakers. This would help stimulate back and forth between the different projects and the audience. If you are interested in a particular topic and would like to help with the organization, please send an e-mail to the BOSC mailing list: bosc(a)lists.open-bio.org. We're also open to new topic suggestions, and will look to add one or two more topics to our current list. Finally, there will be a two day coding session prior to BOSC as a follow up to last year's fun and productive Codefest: http://www.open-bio.org/wiki/Codefest_2011 The Metalab, a unique hacker space in Vienna, has kindly agreed to host us for the two days. If you are at all interested, please add your name to the attendees list on the wiki. Since the Metalab organizers don't know us personally, we'd like to demonstrate there is interest and that we'll really show up with a bunch of bioinformatics hackers. More details will be in the works as the summer draws closer. Looking forward to the sound of music, Brad

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Configuring remote galaxy job runners
by Ry4an Brase 24 Feb '11

24 Feb '11

I'm working on getting more of our jobs offloaded to other machines, and I'm getting job failures I'm not able to debug. When running a simple tool like 'cut', submitted over qsub, I'm getting STDERR output like this: WARNING:galaxy.datatypes.registry:Error loading datatype "binseq.zip", problem: 'module' object has no attribute 'Binseq' WARNING:galaxy.datatypes.registry:Error loading datatype "fastqc", problem: 'module' object has no attribute 'fastqc' WARNING:galaxy.datatypes.registry:Error loading datatype "ssaha2_index", problem: 'module' object has no attribute 'SSAHA2Index' and nothing on STDOUT. I'm doing the "Unified Method" as described here https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster with paths to datafiles and executables the same on the web runner and torque worker systems. I can successfully qsub trivial jobs ("ls") from the web runner machine and see them executed remotely. The web runner's galaxy log doesn't show anything out of the norm: galaxy.jobs INFO 2011-02-23 16:23:55,400 JobWrapper prepare 4019 Cut1 Ry4an perl /website/galaxy.msi.umn.edu/PRODUCTION/tools/filters/cutWrapper.pl /galaxy/PRODUCTION/database/files/019/dataset_19366.dat "c1,c2" T /galaxy/PRODUCTION/database/files/019/dataset_19823.dat galaxy.jobs INFO 2011-02-23 16:24:04,559 JobWrapper state 4019 Cut1 running Ry4an 128.101.189.29 - - [23/Feb/2011:16:24:06 -0500] "POST /root/history_item_updates HTTP/1.1" 200 - "https://galaxy.msi.umn.edu/history" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/534.13 (KHTML, like Gecko) Chrome/9.0.597.84 Safari/534.13" galaxy.jobs INFO 2011-02-23 16:24:07,771 JobWrapper finish 4019 Cut1 error Ry4an galaxy.jobs INFO 2011-02-23 16:24:07,880 JobWrapper done 4019 Cut1 error Ry4an I didn't see it in the Cluster config but I added the <galaxyroot>/lib to the $PYTHONPATH just in case, but no luck. Is it possible it's just the output on STDERR causing the job to fail, and if so how do I shut that up when I'm running through qsub (so redirect to /dev/null isn't quite right)? Thanks, -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

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Trouble compiling SAMtools
by Zachariah K Zachariah 24 Feb '11

24 Feb '11

Hello, I am having some trouble compiling SAMtools on a Solaris10 X86 p latform using gcc compiler version 3.4.6. Using the Makefile I get some link errors and have not been successful in creating the binary or the associated libraries. It seemed to me that it was missing the socket library. I tried adding -lsocket to the compile directive but landed up with no resolution. Here is a transcript of the make command used to build the binary file. I'd sure appreciate some help/pointers from experienced people of this list. Thanks in advance. root >> make make[1]: Entering directory `/home/zkzac/samtools-0.1.12a' make[2]: Entering directory `/home/zkzac/samtools-0.1.12a' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o bam_import.c: In function `append_text': bam_import.c:179: warning: long int format, size_t arg (arg 3) bam_import.c:186: warning: long int format, size_t arg (arg 3) bam_import.c:186: warning: long int format, size_t arg (arg 4) bam_import.c:186: warning: long int format, size_t arg (arg 5) bam_import.c:186: warning: long int format, size_t arg (arg 6) gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o make[2]: Leaving directory `/home/zkzac/samtools-0.1.12a' make[2]: Entering directory `/home/zkzac/samtools-0.1.12a/bcftools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o bcfutils.c: In function `bcf_shrink_alt': bcfutils.c:64: warning: implicit declaration of function `alloca' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o prob1.c: In function `cal_pdg': prob1.c:189: warning: implicit declaration of function `alloca' prob1.c: In function `mc_cal_afs': prob1.c:340: warning: implicit declaration of function `isinf' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o ld.o kfunc.o index.o fet.o bcf2qcall.o make[2]: Leaving directory `/home/zkzac/samtools-0.1.12a/bcftools' make[2]: Entering directory `/home/zkzac/samtools-0.1.12a/misc' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/home/zkzac/samtools-0.1.12a/misc' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o bam_tview.c:7:2: warning: #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled" bam_tview.c:418:2: warning: #warning "No curses library is available; tview is disabled." gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o bam2bcf_indel.c: In function `bcf_call_gap_prep': bam2bcf_indel.c:326: warning: implicit declaration of function `alloca' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -g -Wall -O2 -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf Undefined first referenced symbol in file socket libbam.a(knetfile.o) setsockopt libbam.a(knetfile.o) connect libbam.a(knetfile.o) getaddrinfo libbam.a(knetfile.o) freeaddrinfo libbam.a(knetfile.o) ld: fatal: Symbol referencing errors. No output written to samtools collect2: ld returned 1 exit status make[1]: *** [samtools] Error 1 make[1]: Leaving directory `/home/zkzac/samtools-0.1.12a' make: *** [all-recur] Error 1

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Re: [galaxy-dev] [galaxy-user] Map with Bowtie for Illumina
by Dannon Baker 24 Feb '11

24 Feb '11

Moving this to the galaxy-dev mailing list since it's about a local Galaxy installation. The error here is likely a misconfigured tool_data_table_conf.xml. The format of this file has changed, see the tool_data_table_conf.xml.sample for an example of the new structure. Let me know if your file looks correct with the new format and you're still having issues. -Dannon On Feb 23, 2011, at 2:24 PM, Sonali Thakur wrote: > Hello, > > We are getting below error with the Map with Bowtie for Illumina tool. > Please suggest. > > Traceback (most recent call last): > File "/var/www/galaxy/lib/galaxy/jobs/runners/local.py", line 55, in run_job > job_wrapper.prepare() > File "/var/www/galaxy/lib/galaxy/jobs/__init__.py", line 347, in prepare > self.command_line = self.tool.build_command_line( param_dict ) > File "/var/www/galaxy/lib/galaxy/tools/__init__.py", line 1515, in build_command_line > command_line = fill_template( self.command, context=param_dict ) > File "/var/www/galaxy/lib/galaxy/util/template.py", line 9, in fill_template > return str( Template( source=template_text, searchList=[context] ) ) > File "/var/www/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ > return getattr(self, mainMethName)() > File "DynamicallyCompiledCheetahTemplate.py", line 222, in respond > IndexError: list index out of range > > Thanks > _______________________________________________ > The Galaxy User list should be used for the discussion > of Galaxy analysis and other features on the public > server at usegalaxy.org. For discussion of local Galaxy > instances and the Galaxy source code, please use the > Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/

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Map with Bowtie for Illumina tool
by Sonali Thakur 24 Feb '11

24 Feb '11

Hello, We are getting below error with the Map with Bowtie for Illumina<http://rave.cshl.edu/galaxy/tool_runner?tool_id=bowtie_wrapper>tool. Please suggest. Traceback (most recent call last): File "/var/www/galaxy/lib/galaxy/ jobs/runners/local.py", line 55, in run_job job_wrapper.prepare() File "/var/www/galaxy/lib/galaxy/jobs/__init__.py", line 347, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/var/www/galaxy/lib/galaxy/tools/__init__.py", line 1515, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/var/www/galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/var/www/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 222, in respond IndexError: list index out of range Thanks

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MACS 1.4
by Ryan Golhar 24 Feb '11

24 Feb '11

Does anyone have an updated tool-runner .XML and .py for MACS 1.4? It looks like Galaxy uses an older version of MACS. -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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config files
by Glen Beane 24 Feb '11

24 Feb '11

We run a local galaxy instance with multiple galaxy web servers and a job runner. Per the wiki suggestion we have two config files: universe_wsgi.webapp.ini and universe_wsgi.runner.ini. I've noticed that we still need universe_wsgi.ini or else galaxy will not start Instead of maintaining three config files (which are nearly identical) it would be really helpful if we could just have a single config file. As far as I can tell, the only thing preventing me from doing this is the "enable_job_running" option. If this were a server parameter, then I could have a single config file. Something like this: [server:runner] use = egg:Paste#http port = 8079 host = 0.0.0.0 use_threadpool = true threadpool_workers = 3 enable_job_running = True [server:web0] use = egg:Paste#http port = 8080 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 enable_job_running = False [server:web1] use = egg:Paste#http port = 8081 host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 enable_job_running = False ... [server:webN] use = egg:Paste#http port = 808X host = 0.0.0.0 use_threadpool = true threadpool_workers = 7 enable_job_running = False With a single file I wouldn't have to figure out which of our config file(s) a new setting needs to go into, I can just make the change once

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by George Marselis 23 Feb '11

23 Feb '11

---- George Marselis, systems administrator Building #2, Level 4, room 4327 Computational Bioscience Research Center, KAUST Land: +966-2-808-2944, Mobile: +966-56-321-7714, Skype: project2501a

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