1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4524c1a80fae/
changeset: r5533:4524c1a80fae
user: fubar
date: 2011-05-10 16:35:19
summary: added all_fasta.loc to buildbot - needed for picard tests
affected #: 1 file (36 bytes)
--- a/buildbot_setup.sh Tue May 10 10:31:49 2011 -0400
+++ b/buildbot_setup.sh Tue May 10 10:35:19 2011 -0400
@@ -28,6 +28,7 @@
LINKS="
/galaxy/data/location/add_scores.loc
+/galaxy/data/location/all_fasta.loc
/galaxy/data/location/alignseq.loc
/galaxy/data/annotation_profiler
/galaxy/data/annotation_profiler/annotation_profiler.loc
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/aad64f351785/
changeset: r5532:aad64f351785
user: fubar
date: 2011-05-10 16:31:49
summary: relax number of lines_diff in insertsize test
affected #: 1 file (0 bytes)
--- a/tools/picard/rgPicardInsertSize.xml Mon May 09 22:29:17 2011 -0400
+++ b/tools/picard/rgPicardInsertSize.xml Tue May 10 10:31:49 2011 -0400
@@ -31,7 +31,7 @@
<param name="tailLimit" value="10000" /><param name="histWidth" value="0" /><param name="minPct" value="0.01" />
- <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="30" />
+ <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="35" /></test></tests><help>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/fd3391bcd903/
changeset: r5531:fd3391bcd903
user: dan
date: 2011-05-10 04:29:17
summary: Fixes for Picard: ReorderSam.
affected #: 1 file (9 bytes)
--- a/tools/picard/picard_ReorderSam.xml Mon May 09 16:51:14 2011 -0400
+++ b/tools/picard/picard_ReorderSam.xml Mon May 09 22:29:17 2011 -0400
@@ -16,11 +16,11 @@
--allow-contig-len-discord=$allowContigLenDiscord
--output-format=$outputFormat
#if str( $outputFormat ) == "sam"
- --output-sam=$outFileSam
+ --output=$outFileSam
#else if str( $outputFormat ) == "bam"
- --output-sam=$outFileBam
+ --output=$outFileBam
#end if
- -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard-1.41.jar"
+ -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar"
--picard-cmd="ReorderSam"
</command><inputs>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new changesets in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/92d725e1a392/
changeset: r5521:92d725e1a392
user: kellyv
date: 2011-05-09 17:11:23
summary: Adding picard loc file to buildbot setup
affected #: 1 file (39 bytes)
--- a/buildbot_setup.sh Fri Apr 22 15:10:04 2011 -0400
+++ b/buildbot_setup.sh Mon May 09 11:11:23 2011 -0400
@@ -53,6 +53,7 @@
/galaxy/data/location/perm_base_index.loc
/galaxy/data/location/perm_color_index.loc
/galaxy/data/location/phastOdds.loc
+/galaxy/data/location/picard_index.loc
/galaxy/data/location/quality_scores.loc
/galaxy/data/location/regions.loc
/galaxy/data/location/sam_fa_indices.loc
http://bitbucket.org/galaxy/galaxy-central/changeset/5a446b4344f9/
changeset: r5522:5a446b4344f9
user: kellyv
date: 2011-05-09 17:13:42
summary: merge
affected #: 105 files (1.0 MB)
Diff too large to display.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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