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[hg] galaxy 3038: Explicitly check eggs and fetch when starting, ...
by Greg Von Kuster 17 Nov '09

17 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/56f0d16aa299 changeset: 3038:56f0d16aa299 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Nov 16 14:42:09 2009 -0500 description: Explicitly check eggs and fetch when starting, instead of relying on automatic in-process fetching. Also contains a fix for pysqlite egg building diffstat: run.sh | 19 +++++++++++++++++++ scripts/check_eggs.py | 14 +++++++++++--- scripts/scramble/scripts/pysqlite.py | 2 +- 3 files changed, 31 insertions(+), 4 deletions(-) diffs (71 lines): diff -r 3d0e1bdd6ce1 -r 56f0d16aa299 run.sh --- a/run.sh Mon Nov 16 11:27:30 2009 -0500 +++ b/run.sh Mon Nov 16 14:42:09 2009 -0500 @@ -1,4 +1,23 @@ #!/bin/sh cd `dirname $0` + +# explicitly attempt to fetch eggs before running +FETCH_EGGS=1 +for arg in "$@"; do + [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break +done +if [ $FETCH_EGGS -eq 1 ]; then + python -ES ./scripts/check_eggs.py quiet + if [ $? -ne 0 ]; then + echo "Some eggs are out of date, attempting to fetch..." + python -ES ./scripts/fetch_eggs.py + if [ $? -eq 0 ]; then + echo "Fetch successful." + else + echo "Fetch failed." + exit 1 + fi + fi +fi python -ES ./scripts/paster.py serve universe_wsgi.ini $@ diff -r 3d0e1bdd6ce1 -r 56f0d16aa299 scripts/check_eggs.py --- a/scripts/check_eggs.py Mon Nov 16 11:27:30 2009 -0500 +++ b/scripts/check_eggs.py Mon Nov 16 14:42:09 2009 -0500 @@ -11,6 +11,12 @@ lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) +try: + assert sys.argv[1] == 'quiet' + quiet = True +except: + quiet = False + from galaxy.eggs import * c = Crate() @@ -21,7 +27,9 @@ if not galaxy_config.check_conditional( name ): ignore.append( name ) if not c.find( ignore=ignore ): - print "Some of your Galaxy eggs are out of date. Please update them" - print "by running:" - print " python scripts/fetch_eggs.py" + if not quiet: + print "Some of your Galaxy eggs are out of date. Please update them" + print "by running:" + print " python scripts/fetch_eggs.py" sys.exit( 1 ) +sys.exit( 0 ) diff -r 3d0e1bdd6ce1 -r 56f0d16aa299 scripts/scramble/scripts/pysqlite.py --- a/scripts/scramble/scripts/pysqlite.py Mon Nov 16 11:27:30 2009 -0500 +++ b/scripts/scramble/scripts/pysqlite.py Mon Nov 16 14:42:09 2009 -0500 @@ -33,10 +33,10 @@ # tag me = sys.argv[0] sys.argv = [ me ] +sys.argv.append( "build_static" ) if tag is not None: sys.argv.append( "egg_info" ) sys.argv.append( "--tag-build=%s" %tag ) -sys.argv.append( "build_static" ) sys.argv.append( "bdist_egg" ) # go

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[hg] galaxy 3037: Fix unicode error in data.display_info(). Fixe...
by Greg Von Kuster 17 Nov '09

17 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3d0e1bdd6ce1 changeset: 3037:3d0e1bdd6ce1 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 16 11:27:30 2009 -0500 description: Fix unicode error in data.display_info(). Fixes #226. diffstat: lib/galaxy/datatypes/data.py | 5 +++++ 1 files changed, 5 insertions(+), 0 deletions(-) diffs (15 lines): diff -r b7c6a418c571 -r 3d0e1bdd6ce1 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Mon Nov 16 10:57:31 2009 -0500 +++ b/lib/galaxy/datatypes/data.py Mon Nov 16 11:27:30 2009 -0500 @@ -160,6 +160,11 @@ info = info.replace( '\r', '<br/>' ) if info.find( '\n' ) >= 0: info = info.replace( '\n', '<br/>' ) + + # Convert to unicode to display non-ascii characters. + if type( info ) is not unicode: + info = unicode( info, 'utf-8') + return info except: return "info unavailable"

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[hg] galaxy 3040: merge
by Greg Von Kuster 17 Nov '09

17 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/84f96ae27ef4 changeset: 3040:84f96ae27ef4 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 16 14:52:51 2009 -0500 description: merge diffstat: run.sh | 19 +++++++++++++++++++ scripts/check_eggs.py | 14 +++++++++++--- scripts/scramble/scripts/pysqlite.py | 2 +- 3 files changed, 31 insertions(+), 4 deletions(-) diffs (71 lines): diff -r 052f6096e3cd -r 84f96ae27ef4 run.sh --- a/run.sh Mon Nov 16 14:52:33 2009 -0500 +++ b/run.sh Mon Nov 16 14:52:51 2009 -0500 @@ -1,4 +1,23 @@ #!/bin/sh cd `dirname $0` + +# explicitly attempt to fetch eggs before running +FETCH_EGGS=1 +for arg in "$@"; do + [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break +done +if [ $FETCH_EGGS -eq 1 ]; then + python -ES ./scripts/check_eggs.py quiet + if [ $? -ne 0 ]; then + echo "Some eggs are out of date, attempting to fetch..." + python -ES ./scripts/fetch_eggs.py + if [ $? -eq 0 ]; then + echo "Fetch successful." + else + echo "Fetch failed." + exit 1 + fi + fi +fi python -ES ./scripts/paster.py serve universe_wsgi.ini $@ diff -r 052f6096e3cd -r 84f96ae27ef4 scripts/check_eggs.py --- a/scripts/check_eggs.py Mon Nov 16 14:52:33 2009 -0500 +++ b/scripts/check_eggs.py Mon Nov 16 14:52:51 2009 -0500 @@ -11,6 +11,12 @@ lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) +try: + assert sys.argv[1] == 'quiet' + quiet = True +except: + quiet = False + from galaxy.eggs import * c = Crate() @@ -21,7 +27,9 @@ if not galaxy_config.check_conditional( name ): ignore.append( name ) if not c.find( ignore=ignore ): - print "Some of your Galaxy eggs are out of date. Please update them" - print "by running:" - print " python scripts/fetch_eggs.py" + if not quiet: + print "Some of your Galaxy eggs are out of date. Please update them" + print "by running:" + print " python scripts/fetch_eggs.py" sys.exit( 1 ) +sys.exit( 0 ) diff -r 052f6096e3cd -r 84f96ae27ef4 scripts/scramble/scripts/pysqlite.py --- a/scripts/scramble/scripts/pysqlite.py Mon Nov 16 14:52:33 2009 -0500 +++ b/scripts/scramble/scripts/pysqlite.py Mon Nov 16 14:52:51 2009 -0500 @@ -33,10 +33,10 @@ # tag me = sys.argv[0] sys.argv = [ me ] +sys.argv.append( "build_static" ) if tag is not None: sys.argv.append( "egg_info" ) sys.argv.append( "--tag-build=%s" %tag ) -sys.argv.append( "build_static" ) sys.argv.append( "bdist_egg" ) # go

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[hg] galaxy 3036: Have Extract Genomic DNA tool copy metadata fr...
by Greg Von Kuster 17 Nov '09

17 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b7c6a418c571 changeset: 3036:b7c6a418c571 user: dan date: Mon Nov 16 10:57:31 2009 -0500 description: Have Extract Genomic DNA tool copy metadata from input file. This will allow the tool to keep column assignments when outputing interval format. diffstat: tools/extract/extract_genomic_dna.xml | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (18 lines): diff -r 1f8542d78671 -r b7c6a418c571 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml Sat Nov 14 20:32:41 2009 -0500 +++ b/tools/extract/extract_genomic_dna.xml Mon Nov 16 10:57:31 2009 -0500 @@ -1,4 +1,4 @@ -<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.0"> +<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.1"> <description>using coordinates from assembled/unassembled genomes</description> <command interpreter="python">extract_genomic_dna.py $input $out_file1 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command> <inputs> @@ -12,7 +12,7 @@ </param> </inputs> <outputs> - <data format="fasta" name="out_file1"> + <data format="fasta" name="out_file1" metadata_source="input"> <change_format> <when input="out_format" value="interval" format="interval" /> </change_format>

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Fastx toolkit
by juan perin 16 Nov '09

16 Nov '09

My installation of the fastx toolkit seems to be having quite a few problems. I can run the groomer on my data, although it seems to remove a lot more data than expected. I often end up with empty files. More concerning right now is the attempt to calculate quality statistics. These never work for me, although I've been able to get it to work on the main PSU galaxy instance with the same data. Command line usage fails with the same error: fastx_quality_stats: Invalid quality score value (char '%' ord 37 quality value -27) on line 4 * * *The error may be misleading, but its all I can gather from any out put right now. It may be more appropriate to ask this to someone in the FASTX community, but figured I'd shoot here as well, in case this has come up before. * * * *Thanks!* * * *Juan Perin* * *

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Questions about Galaxy!
by WangJun 16 Nov '09

16 Nov '09

Hi, This is a question about Galaxy interaction with UCSC data. I hava a dataset platform, and I want to add a button like the UCSC's "Send query to Galaxy". I find that it's actually a form: <form method="POST" action="http://main.g2.bx.psu.edu/tool_runner"> <input type="HIDDEN" value="ucsc_table_direct1" name="tool_id"/> <input type="HIDDEN" value="http://genome.ucsc.edu/cgi-bin/hgTables" name="URL"/> <input type="HIDDEN" value="296389734" name="hguid"/> <input type="HIDDEN" value="hg18" name="db"/> <input type="HIDDEN" value="Human" name="org"/> <input type="HIDDEN" value="multiz28way" name="hgta_table"/> <input type="HIDDEN" value="multiz28way" name="hgta_track"/> <input type="HIDDEN" value="range" name="hgta_regionType"/> <input type="HIDDEN" value="primaryTable" name="hgta_outputType"/> <input type="HIDDEN" value="chr3:130734948-130736581" name="position"/> <input type="HIDDEN" value="get output" name="hgta_doTopSubmit"/> <input type="HIDDEN" value="146683120" name="hgsid"/> <input type="SUBMIT" value="Send query to Galaxy" name="hgta_doGalaxyQuery"/> </form> I have a url and three params, and I tried. But I can't see my data in the right-side green box. And what's the tool_id param used for? Thanks in advance! Best, Kathleen 2009-11-16

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Failure in functional test
by Vipin TS 16 Nov '09

16 Nov '09

Hi , I wrote a functional test for my galaxy tool. While running the functional tests it shows the following error message. Failure: ValueError (No such test TestForTool_gentool) ... ERROR ====================================================================== ERROR: Failure: ValueError (No such test TestForTool_gentool) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/myhome/galaxy-0/eggs/py2.5-noplatform/nose-0.11.1-py2.5.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_gentool ---------------------------------------------------------------------- Ran 1 test in 0.002s FAILED (errors=1) >From exception I can find that there is no test case for gentool. But I have one test case for the same. and here is my test which I wrote. <tests> <test> <param name="source" value="history" /> <param name="fasta_input" value="tair9_chr4.fas" ftype="fasta" /> <output name="output" file="tair9_chr4.gio" /> </test> </tests> Many thanks in advance, Vipin T S

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Fwd: Failure in functional test
by Vipin TS 16 Nov '09

16 Nov '09

Hi Nate, Yes. <tool id="gentool" name="GenomeTool"> To run the tests, I am using sh run_functional_tests.sh -id gentool Yes, It is loading into my galaxy instance and I can run the tool through the web browser. Here I am including the error message which I got from run_functional_tests.html file File "/usr/lib/python2.5/unittest.py", line 260, in run testMethod() File "/home/galaxy/galaxy-2.1.2009/eggs/py2.5-noplatform/nose-0.11.1-py2.5.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) ValueError: No such test TestForTool_gentool Hope this will help you. Thanks for your time. Vipin T S

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[hg] galaxy 3035: Fix for cleanup_datasets.py - add app param to...
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1f8542d78671 changeset: 3035:1f8542d78671 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Sat Nov 14 20:32:41 2009 -0500 description: Fix for cleanup_datasets.py - add app param to the _purge_dataset method signature. diffstat: scripts/cleanup_datasets/cleanup_datasets.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r 1bef953daabf -r 1f8542d78671 scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Fri Nov 13 17:19:44 2009 -0500 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Sat Nov 14 20:32:41 2009 -0500 @@ -276,7 +276,7 @@ app.model.Dataset.table.c.update_time < cutoff_time ) ) for dataset in datasets: file_size = dataset.file_size - _purge_dataset( dataset, remove_from_disk, info_only = info_only ) + _purge_dataset( app, dataset, remove_from_disk, info_only = info_only ) dataset_count += 1 try: disk_space += file_size @@ -349,7 +349,7 @@ app.sa_session.add( dataset ) app.sa_session.flush() -def _purge_dataset( dataset, remove_from_disk, info_only = False ): +def _purge_dataset( app, dataset, remove_from_disk, info_only = False ): if dataset.deleted: try: if dataset.purgable and _dataset_is_deletable( dataset ):

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[hg] galaxy 3034: Support Solaris 10 x86 as well.
by Greg Von Kuster 16 Nov '09

16 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1bef953daabf changeset: 3034:1bef953daabf user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Nov 13 17:19:44 2009 -0500 description: Support Solaris 10 x86 as well. diffstat: dist-eggs.ini | 9 ++++++--- 1 files changed, 6 insertions(+), 3 deletions(-) diffs (26 lines): diff -r e8a116c6bd96 -r 1bef953daabf dist-eggs.ini --- a/dist-eggs.ini Fri Nov 13 17:08:12 2009 -0500 +++ b/dist-eggs.ini Fri Nov 13 17:19:44 2009 -0500 @@ -23,6 +23,9 @@ py2.5-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.5 py2.6-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.6 py2.5-macosx-10.5-i386-ucs2 = lion.bx.psu.edu /usr/bin/python2.5 +py2.4-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /depot/projects/pythons/solaris-2.10-i86pc-ucs2/bin/python2.4 +py2.5-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /depot/projects/pythons/solaris-2.10-i86pc-ucs2/bin/python2.5 +py2.6-solaris-2.10-i86pc-ucs2 = thumper.bx.psu.edu /depot/projects/pythons/solaris-2.10-i86pc-ucs2/bin/python2.6 py2.4-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.4 py2.5-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.5 py2.6-solaris-2.11-i86pc-ucs2 = victory.bx.psu.edu /depot/projects/pythons/solaris-2.11-i86pc-ucs2/bin/python2.6 @@ -47,9 +50,9 @@ py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.5-macosx-10.5-i386-ucs2 py2.6-macosx = py2.6-macosx-10.3-fat-ucs2 macosx = py2.4-macosx py2.5-macosx py2.6-macosx -py2.4-solaris = py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2 -py2.5-solaris = py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2 -py2.6-solaris = py2.6-solaris-2.11-i86pc-ucs2 py2.6-solaris-2.10-sun4u-ucs2 +py2.4-solaris = py2.4-solaris-2.10-i86pc-ucs2 py2.4-solaris-2.11-i86pc-ucs2 py2.4-solaris-2.10-sun4u-ucs2 +py2.5-solaris = py2.5-solaris-2.10-i86pc-ucs2 py2.5-solaris-2.11-i86pc-ucs2 py2.5-solaris-2.10-sun4u-ucs2 +py2.6-solaris = py2.6-solaris-2.10-i86pc-ucs2 py2.6-solaris-2.11-i86pc-ucs2 py2.6-solaris-2.10-sun4u-ucs2 solaris = py2.4-solaris py2.5-solaris py2.6-solaris py2.4-all = py2.4-linux py2.4-macosx py2.4-solaris py2.5-all = py2.5-linux py2.5-macosx py2.5-solaris

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