1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/34fffbf01183/
changeset: 34fffbf01183
user: dan
date: 2011-10-25 21:43:04
summary: Add metadata validator to force input bam files to have bam_index metadata files for GATK tools.
affected #: 6 files
diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/count_covariates.xml
--- a/tools/gatk/count_covariates.xml
+++ b/tools/gatk/count_covariates.xml
@@ -138,6 +138,7 @@
<when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" />
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome">
@@ -147,7 +148,9 @@
</param></when><when value="history"><!-- FIX ME!!!! -->
- <param name="input_bam" type="data" format="bam" label="BAM file" />
+ <param name="input_bam" type="data" format="bam" label="BAM file" >
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+ </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional>
diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/indel_realigner.xml
--- a/tools/gatk/indel_realigner.xml
+++ b/tools/gatk/indel_realigner.xml
@@ -107,6 +107,7 @@
<when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" />
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome">
@@ -116,7 +117,9 @@
</param></when><when value="history"><!-- FIX ME!!!! -->
- <param name="input_bam" type="data" format="bam" label="BAM file" />
+ <param name="input_bam" type="data" format="bam" label="BAM file" >
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+ </param><param name="ref_file" type="data" format="fasta" label="Using reference file"><options><filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! -->
diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/realigner_target_creator.xml
--- a/tools/gatk/realigner_target_creator.xml
+++ b/tools/gatk/realigner_target_creator.xml
@@ -103,6 +103,7 @@
<when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" />
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome">
@@ -112,7 +113,9 @@
</param></when><when value="history">
- <param name="input_bam" type="data" format="bam" label="BAM file" />
+ <param name="input_bam" type="data" format="bam" label="BAM file" >
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+ </param><param name="ref_file" type="data" format="fasta" label="Using reference file"><options><filter type="data_meta" key="dbkey" ref="input_bam" /><!-- FIX ME!!!! -->
diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/table_recalibration.xml
--- a/tools/gatk/table_recalibration.xml
+++ b/tools/gatk/table_recalibration.xml
@@ -117,6 +117,7 @@
<when value="cached"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" />
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome">
@@ -126,7 +127,9 @@
</param></when><when value="history"><!-- FIX ME!!!! -->
- <param name="input_bam" type="data" format="bam" label="BAM file" />
+ <param name="input_bam" type="data" format="bam" label="BAM file" >
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+ </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional>
diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/unified_genotyper.xml
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -135,6 +135,7 @@
<repeat name="input_bams" title="Sample BAM file" min="1"><param name="input_bam" type="data" format="bam" label="BAM file"><validator type="unspecified_build" />
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param></repeat>
@@ -146,7 +147,9 @@
</when><when value="history"><!-- FIX ME!!!! --><repeat name="input_bams" title="Sample BAM file" min="1">
- <param name="input_bam" type="data" format="bam" label="BAM file" />
+ <param name="input_bam" type="data" format="bam" label="BAM file" >
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+ </param></repeat><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when>
diff -r 33bdfafacc0064e3975beb10dd2694d8240bf23a -r 34fffbf01183c5ae9a9037e4a13501c9cf5b8b8d tools/gatk/variant_annotator.xml
--- a/tools/gatk/variant_annotator.xml
+++ b/tools/gatk/variant_annotator.xml
@@ -145,6 +145,7 @@
<param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." /><param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." ><validator type="unspecified_build" />
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/><validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /><!-- fixme!!! this needs to be a select --></param><param name="ref_file" type="select" label="Using reference genome">
@@ -156,7 +157,9 @@
<when value="history"><!-- FIX ME!!!! --><param name="input_variant" type="data" format="vcf" label="Variant file to annotate" /><param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
- <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" />
+ <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" >
+ <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
+ </param><param name="ref_file" type="data" format="fasta" label="Using reference file" /></when></conditional>
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/6010fcf5e677/
changeset: 6010fcf5e677
user: dan
date: 2011-10-25 20:21:49
summary: Remove some debug prints from GATK unified genotyper.
affected #: 1 file
diff -r b0967259b2905e58bc0e75ba8ada7a0cd8974b7d -r 6010fcf5e6773a4f06b148420bf046d3d8a22b4d tools/gatk/unified_genotyper.xml
--- a/tools/gatk/unified_genotyper.xml
+++ b/tools/gatk/unified_genotyper.xml
@@ -7,8 +7,6 @@
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
- ${dir( $input_bam.input_bam )}
- ${dir( $input_bam.input_bam.dataset )}
-d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
#end for
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/b0967259b290/
changeset: b0967259b290
user: dan
date: 2011-10-25 19:58:08
summary: Show dataset size of non-purged error state history items.
affected #: 1 file
diff -r 4d1e525e1594a63221c099c5f84ca5765775533b -r b0967259b2905e58bc0e75ba8ada7a0cd8974b7d templates/root/history_common.mako
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -96,7 +96,7 @@
display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' )
%>
%if data.purged:
- <span class="icon-button display_disabled tooltip" title="Cannoy display datasets removed from disk"></span>
+ <span class="icon-button display_disabled tooltip" title="Cannot display datasets removed from disk"></span>
%else:
<a class="icon-button display tooltip" title="Display data in browser" href="${display_url}"
%if for_editing:
@@ -150,6 +150,9 @@
%endif
</div>
%elif data_state == "error":
+ %if not data.purged:
+ <div>${data.get_size( nice_size=True )}</div>
+ %endif
<div>
An error occurred running this job: <i>${data.display_info().strip()}</i></div>
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/4d1e525e1594/
changeset: 4d1e525e1594
user: dan
date: 2011-10-25 19:51:56
summary: Allow picard_SamToFastq to use input BAM files.
affected #: 1 file
diff -r 5ed5bcad57015ab0b412dcc2648cbfbf1e11bf9e -r 4d1e525e1594a63221c099c5f84ca5765775533b tools/picard/picard_SamToFastq.xml
--- a/tools/picard/picard_SamToFastq.xml
+++ b/tools/picard/picard_SamToFastq.xml
@@ -42,11 +42,11 @@
|| echo "Error running SamToFastq" >&2
</command><inputs>
- <param name="input_sam" type="data" format="sam" label="SAM file" />
+ <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" /><param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." /><param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." /><param name="output_per_read_group_selector" type="select" label="Output per read group">
- <option value="per_sam_file" selected="True">Per SAM file</option>
+ <option value="per_sam_file" selected="True">Per BAM/SAM file</option><!-- <option value="per_read_group">Per Read Group</option> --><validator type="expression" message="Per Read Group selection is not yet implemented">value == 'per_sam_file'</validator></param>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/4421e535870a/
changeset: 4421e535870a
branch: fastq-deinterlacer-memfix
user: natefoo
date: 2011-10-25 16:52:43
summary: Closed fastq-deinterlacer-memfix
affected #: 0 files
https://bitbucket.org/galaxy/galaxy-central/changeset/5ed5bcad5701/
changeset: 5ed5bcad5701
user: natefoo
date: 2011-10-25 16:54:17
summary: Fix Python versions in README.txt
affected #: 1 file
diff -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef -r 5ed5bcad57015ab0b412dcc2648cbfbf1e11bf9e README.txt
--- a/README.txt
+++ b/README.txt
@@ -7,7 +7,7 @@
HOW TO START
============
-Galaxy requires Python 2.4, 2.5 or 2.6. To check your python version, run:
+Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run:
% python -V
Python 2.4.4
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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