1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/31932fa8c0e1/
changeset: 31932fa8c0e1
user: greg
date: 2011-11-25 15:24:58
summary: Remove the old template_path setting from community_wsgi.ini. since it is set incorrecly and not neede anyway.
affected #: 1 file
diff -r ab90893a7cf51e272cafa97b4702d32edb44223f -r 31932fa8c0e1e2f84c54107356487ec427d2a521 community_wsgi.ini.sample
--- a/community_wsgi.ini.sample
+++ b/community_wsgi.ini.sample
@@ -26,9 +26,6 @@
# Temporary storage for additional datasets, this should be shared through the cluster
new_file_path = database/tmp
-# Where templates are stored
-template_path = lib/galaxy/webapps/community/templates
-
# Session support (beaker)
use_beaker_session = True
session_type = memory
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9d6a9963b0da/
changeset: 9d6a9963b0da
user: dan
date: 2011-11-22 18:21:05
summary: Have fimo.xml use fields.path approach instead of directly filtering on data table.
affected #: 1 file
diff -r 49c48236f6ae2d8557420b1393fd763ce5f28889 -r 9d6a9963b0da21fe3139fcefbd11c1ec6290a529 tools/meme/fimo.xml
--- a/tools/meme/fimo.xml
+++ b/tools/meme/fimo.xml
@@ -32,7 +32,7 @@
#if str( $fasta_type.fasta_type_selector ) == 'history':
"${fasta_type.input_database}"
#else:
- "${ filter( lambda x: str( x[0] ) == str( $fasta_type.input_database ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][3] }"
+ "${fasta_type.input_database.fields.path}"
#end if
'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/49c48236f6ae/
changeset: 49c48236f6ae
user: dan
date: 2011-11-22 17:56:53
summary: Have rgPicardGCBiasMetrics.xml use fields.path approach instead of directly filtering on data table.
affected #: 1 file
diff -r 84187b357d0c6b5bf0c2d9bab5609c10143efb75 -r 49c48236f6ae2d8557420b1393fd763ce5f28889 tools/picard/rgPicardGCBiasMetrics.xml
--- a/tools/picard/rgPicardGCBiasMetrics.xml
+++ b/tools/picard/rgPicardGCBiasMetrics.xml
@@ -4,9 +4,9 @@
--windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}"
-j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar
#if $genomeSource.refGenomeSource == "history":
- --ref-file "$genomeSource.ownFile"
+ --ref-file "${genomeSource.ownFile}"
#else:
- --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
+ --ref "${genomeSource.index.fields.path}"
#end if
</command><requirements><requirement type="package">picard</requirement></requirements>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/52ce5e6950b7/
changeset: 52ce5e6950b7
user: dan
date: 2011-11-21 22:55:16
summary: Update help for some SAMTools.
affected #: 5 files
diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/bam_to_sam.xml
--- a/tools/samtools/bam_to_sam.xml
+++ b/tools/samtools/bam_to_sam.xml
@@ -56,5 +56,11 @@
.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
+
</help></tool>
diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/sam_pileup.xml
--- a/tools/samtools/sam_pileup.xml
+++ b/tools/samtools/sam_pileup.xml
@@ -177,6 +177,12 @@
.. _consensus: http://samtools.sourceforge.net/cns0.shtml
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
+
</help></tool>
diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/sam_to_bam.xml
--- a/tools/samtools/sam_to_bam.xml
+++ b/tools/samtools/sam_to_bam.xml
@@ -87,5 +87,11 @@
.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
+
</help></tool>
diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/samtools_flagstat.xml
--- a/tools/samtools/samtools_flagstat.xml
+++ b/tools/samtools/samtools_flagstat.xml
@@ -25,5 +25,13 @@
.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
</help></tool>
diff -r 945c7a47755f4c468d0742ad02d43647a300565c -r 52ce5e6950b7e599b6da104ca5b094df00ea4d26 tools/samtools/samtools_rmdup.xml
--- a/tools/samtools/samtools_rmdup.xml
+++ b/tools/samtools/samtools_rmdup.xml
@@ -57,5 +57,13 @@
.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+------
+
+**Citation**
+
+For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
</help></tool>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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