galaxy-user June 2009

galaxy-user@lists.galaxyproject.org

8 participants
7 discussions

upgrading my local galaxy install
by Erick Antezana 03 Jul '09

03 Jul '09

Hi, I have upgraded my local install by getting the latest source like this: hg pull -u then I compared the *.sample.xml files against my *.xml files (tool_conf.xml). I have also upgraded my DB (from version 6 to 7). I have also launched : sh run_functional_tests.sh and I got a message: ... *** This program requires python version 2.5 or higher *** Current python version is: 2.4.3.final.0 ... I have python 2.4.3. Do I need to upgrade it? During the tests execution I saw the following error messages: ... Test uploading encode data ... ERROR ... ... Gencode Partition ( gencode_partition1 ) > Test-1 ... FAIL ... Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-1 ... FAIL Stitch MAF blocks ( Interval_Maf_Merged_Fasta2 ) > Test-2 ... FAIL ... Summary Statistics ( Summary_Statistics1 ) > Test-1 ... FAIL ... BLAT ( blat_wrapper ) > Test-1 ... FAIL ... Fetch taxonomic representation ( Fetch Taxonomic Ranks ) > Test-1 ... FAIL Poisson two-sample test ( poisson2test ) > Test-1 ... FAIL Poisson two-sample test ( poisson2test ) > Test-2 ... FAIL Compute phastOdds score ( phastOdds_for_intervals ) > Test-1 ... FAIL LAV to BED ( lav_to_bed1 ) > Test-1 ... FAIL ... FAILED (failures=38, errors=5) the rest are OK, some errors and failures I guess are due to the fact that I do not have some tools installed (e.g. BLAT) Do I need to perform any other operation in order to upgrate my local install? (what about the "eggs"? Do I need to check for egg updates? how?) thanks, Erick

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Running gops_cluster.py on the command line fails
by Daniel Gerlach 30 Jun '09

30 Jun '09

Dear Galaxy Team, I followed the instructions and downloaded the Galaxy distribution according to the WIKI. As I do want to run some specific tools locally on the shell, I put import sys and sys.path.append("/somedir/galaxy/lib") before the galaxy module is loaded. However the tool seems not to work and still gives me some errors which I can not figure out. I'd be thankful for some ideas. $ python /somedir/galaxy/tools/new_operations/gops_cluster.py Traceback (most recent call last): File "/home/cegg/gerlach/bin/galaxy/tools/new_operations/gops_cluster.py", line 22, in ? from galaxy.tools.util.galaxyops import * File "/home/cegg/gerlach/bin/galaxy/lib/galaxy/tools/__init__.py", line 16, in ? from galaxy.util.template import fill_template File "/home/cegg/gerlach/bin/galaxy/lib/galaxy/util/template.py", line 2, in ? pkg_resources.require( "Cheetah" ) File "/home/cegg/gerlach/bin/galaxy/lib/galaxy/eggs/__init__.py", line 544, in require sys.path.remove(entry) ValueError: list.remove(x): x not in list With best regrads, Daniel -- Daniel Gerlach, PhD student Computational Evolutionary Genomics Group (CEGG) email: daniel.gerlach(a)unige.ch www: http://cegg.unige.ch/

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Join EST and Refseq
by Massimo 29 Jun '09

29 Jun '09

Hi, I am trying to join a list of EST generated by UCSC Table (user track) with all bovine Refseq list generated as well from UCSC. The two do not share any common column and I cannot have the EST with the associated Refseq. As suggested by people at UCSC I have generated my list of custom track EST and then I have set the group mRNA and EST track, track mRNA, Table RefSeq gene (reGene) and I have done an intersection with all my ESTs (All refGene records that have any overlap with User Track ). I have then send everything to Galaxy and try to use the join two queries feature but I cannot obtain a unique table with both Refseq and EST accession numbers. I have contacted the people from UCSC but they said that there is a way through Galaxy..but I could not figured it out. Please, let me know if there is a way. Thanks in advance for your help! Massimo Bionaz PhD Post-doctoral researcher Institute for Genomic Biology, University of Illinois 366 Animal Sciences Laboratory 1207 W. Gregory Dr. Urbana, IL 61801 USA Office Tel: 1-217-333-6189 Fax: 1-217-333-8286

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string input contains "~"
by R 22 Jun '09

22 Jun '09

Hi, My string type input includes "~", but I found galaxy turned it into "X", so my tool failed to run for the wrong input. Does anyone know how to fix it? Thanks!

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mapping
by Marcus Ludwig 10 Jun '09

10 Jun '09

Hi, I want to map a set of sequences (derived from RNA) against a bacterial genome. Unfortunately, the genome of Synechococcus sp. PCC 7002 consists of one chromosome and six plasmids. In MAQ I can chose only one DNA entry for mapping. In local BLAST it was possible to generate databases consisting of several DNA entries to map the data. Does anybody have experience in mapping transcription data against complex genomes in Galaxy. Best regards, Marcus

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An idea for sharing tools
by James Casbon 10 Jun '09

10 Jun '09

Hi Everyone, I have an "I want a pony" idea that I would like to kick onto the mailing list: It would be great if there was a way for sharing tool definitions between users. At the moment, the main repo is maintained by the galaxy team, and that is fine and makes sense. However, I'm sure there is a lot of duplicated work between the users when adding other tools in. For example, there was a conversation the other day about adding in awk. Someone had already done this, so the best idea would be if I could pull in that definition and enable it with minimum effort. I have already added tools (exonerate, restriction mapper, etc, etc) that may be of use to other people. Not sure the best way to go about this, but if my understanding of mercurial is right, we can simply offer another repo for people to pull changes from. If this is of interest to you, please can you reply? If we get enough interest and preferably some support of the core team, I could set up a free repo at, e.g., bitbucket and add users to it. Or perhaps there is a better way (eg patches submitted to trac)? Another question is what kind of tools would the core team accept for inclusion in the main dist? Cheers, James

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Exception when using remote_user.
by MORITA Hideyuki 10 Jun '09

10 Jun '09

Hi, The following error will occur under certain condition when using remote_user. AttributeError: 'NoneType' object has no attribute 'user' This error is thrown when: 1. using remote_user 2. browser has a valid session (cookie) 3. after logged in with an email address other than previously used This is caused by None value in prev_galaxy_session variable at L.231 in lib/galaxy/web/framework/__init__.py. I understand that galaxy_session instead of prev_galaxy_session should be referenced here. I created a patch to fix this problem by replacing prev_galaxy_session with galaxy_session. =================================================================================== diff -r a4214de3752e lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Feb 03 18:34:27 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Feb 16 13:31:02 2009 +0900 @@ -228,7 +228,7 @@ class UniverseWebTransaction( base.Defau invalidate_existing_session = True user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, prev_galaxy_session.user.email ) + remote_user_email, galaxy_session.user.email ) else: # No session exists, get/create user for new session user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) =================================================================================== Thanks. MORITA Hideyuki

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galaxy-user June 2009