October 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Add metadata validator to force input bam files to have bam_index metadata files for GATK tools.
by Bitbucket 25 Oct '11

25 Oct '11

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." /></param><param name="ref_file" type="select" label="Using reference genome"> @@ -147,7 +148,9 @@ </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" /></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." /></param><param name="ref_file" type="select" label="Using reference genome"> @@ -116,7 +117,9 @@ </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" /> 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." /></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" /> 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." /></param><param name="ref_file" type="select" label="Using reference genome"> @@ -126,7 +127,9 @@ </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" /></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." /></param></repeat> @@ -146,7 +147,9 @@ </when><when value="history"><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." /></param><param name="ref_file" type="select" label="Using reference genome"> @@ -156,7 +157,9 @@ <when value="history"><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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Set URL for visualization when it is first saved.
by Bitbucket 25 Oct '11

25 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/33bdfafacc00/ changeset: 33bdfafacc00 user: jgoecks date: 2011-10-25 21:23:45 summary: Set URL for visualization when it is first saved. affected #: 2 files diff -r 8c7f2c84bbbd084bfbc3edfe64e5a159080145dd -r 33bdfafacc0064e3975beb10dd2694d8240bf23a lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -663,7 +663,8 @@ vis.latest_revision = vis_rev session.add( vis_rev ) session.flush() - return trans.security.encode_id(vis.id) + encoded_id = trans.security.encode_id(vis.id) + return { "id": encoded_id, "url": url_for( action='browser', id=encoded_id ) } @web.expose @web.require_login( "see all available libraries" ) diff -r 8c7f2c84bbbd084bfbc3edfe64e5a159080145dd -r 33bdfafacc0064e3975beb10dd2694d8240bf23a templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -212,10 +212,14 @@ 'dbkey': view.dbkey, 'payload': JSON.stringify(payload) }, - success: function(vis_id) { - view.vis_id = vis_id; + dataType: "json", + success: function(vis_info) { + hide_modal(); + view.vis_id = vis_info.vis_id; view.has_changes = false; - hide_modal(); + + // Needed to set URL when first saving a visualization. + window.history.pushState({}, "", vis_info.url); }, error: function() { alert("Could not save visualization"); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: automatically remove spaces from an entered location.
by Bitbucket 25 Oct '11

25 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8c7f2c84bbbd/ changeset: 8c7f2c84bbbd user: jgoecks date: 2011-10-25 20:59:19 summary: Trackster: automatically remove spaces from an entered location. affected #: 1 file diff -r 6010fcf5e6773a4f06b148420bf046d3d8a22b4d -r 8c7f2c84bbbd084bfbc3edfe64e5a159080145dd static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -1189,6 +1189,10 @@ } }, go_to: function(str) { + // Preprocess str to remove spaces and commas. + str = str.replace(/ |,/g, ""); + + // Go to new location. var view = this, new_low, new_high, @@ -1199,8 +1203,8 @@ if (pos !== undefined) { try { var pos_split = pos.split("-"); - new_low = parseInt(pos_split[0].replace(/,/g, ""), 10); - new_high = parseInt(pos_split[1].replace(/,/g, ""), 10); + new_low = parseInt(pos_split[0], 10); + new_high = parseInt(pos_split[1], 10); } catch (e) { return false; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Remove some debug prints from GATK unified genotyper.
by Bitbucket 25 Oct '11

25 Oct '11

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Show dataset size of non-purged error state history items.
by Bitbucket 25 Oct '11

25 Oct '11

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow picard_SamToFastq to use input BAM files.
by Bitbucket 25 Oct '11

25 Oct '11

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><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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 25 Oct '11

25 Oct '11

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/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update Picard tools to use tool-data/shared/jars/picard/* instead of just tool-data/shared/jars/*.
by Bitbucket 25 Oct '11

25 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/18f2b18d48e8/ changeset: 18f2b18d48e8 user: dan date: 2011-10-25 16:34:35 summary: Update Picard tools to use tool-data/shared/jars/picard/* instead of just tool-data/shared/jars/*. affected #: 14 files diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_AddOrReplaceReadGroups.xml --- a/tools/picard/picard_AddOrReplaceReadGroups.xml +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml @@ -1,4 +1,4 @@ -<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.0"> +<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -15,7 +15,7 @@ #end if --output-format=$outputFormat --output=$outFile - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/AddOrReplaceReadGroups.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/AddOrReplaceReadGroups.jar" </command><inputs><param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in" diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_BamIndexStats.xml --- a/tools/picard/picard_BamIndexStats.xml +++ b/tools/picard/picard_BamIndexStats.xml @@ -1,4 +1,4 @@ -<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.0"> +<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -6,7 +6,7 @@ --bai-file "$input_file.metadata.bam_index" -t "$htmlfile" -d "$htmlfile.files_path" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/BamIndexStats.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/BamIndexStats.jar" </command><inputs><param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for" diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_FastqToSam.xml --- a/tools/picard/picard_FastqToSam.xml +++ b/tools/picard/picard_FastqToSam.xml @@ -1,5 +1,6 @@ <tool id="picard_FastqToSam" name="FASTQ to BAM" version="0.0.1"><description>creates an unaligned BAM file</description> + <requirements><requirement type="package">picard</requirement></requirements><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar" FASTQ="${input_fastq1}" diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_MarkDuplicates.xml --- a/tools/picard/picard_MarkDuplicates.xml +++ b/tools/picard/picard_MarkDuplicates.xml @@ -1,4 +1,4 @@ -<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01"> +<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01.1"><command interpreter="python"> picard_wrapper.py --input="$input_file" @@ -20,7 +20,7 @@ --output-sam=$outFileBamMarked #end if #end if - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/" --picard-cmd="MarkDuplicates" </command><inputs> diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_ReorderSam.xml --- a/tools/picard/picard_ReorderSam.xml +++ b/tools/picard/picard_ReorderSam.xml @@ -1,4 +1,4 @@ -<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.0"> +<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="0.3.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -15,7 +15,7 @@ --allow-contig-len-discord=$allowContigLenDiscord --output-format=$outputFormat --output=$outFile - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReorderSam.jar" </command><inputs><param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered" diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_ReplaceSamHeader.xml --- a/tools/picard/picard_ReplaceSamHeader.xml +++ b/tools/picard/picard_ReplaceSamHeader.xml @@ -1,4 +1,4 @@ -<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.0"> +<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="0.2.1"><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py @@ -6,7 +6,7 @@ -o $outFile --header-file $headerFile --output-format $outputFormat - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReplaceSamHeader.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/ReplaceSamHeader.jar" --tmpdir "${__new_file_path__}" </command><inputs> diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/picard_SamToFastq.xml --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -1,5 +1,6 @@ <tool id="picard_SamToFastq" name="SAM to FASTQ" version="0.0.1"><description>creates a FASTQ file</description> + <requirements><requirement type="package">picard</requirement></requirements><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/SamToFastq.jar" INPUT="${input_sam}" diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -1,8 +1,8 @@ -<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03"> +<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="0.03.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" - -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectAlignmentSummaryMetrics.jar + -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectAlignmentSummaryMetrics.jar #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardFixMate.xml --- a/tools/picard/rgPicardFixMate.xml +++ b/tools/picard/rgPicardFixMate.xml @@ -1,8 +1,8 @@ -<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0"> +<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.1"><description>for paired data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" - --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/FixMateInformation.jar" --sortorder "$sortOrder" + --output-format "$outputFormat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FixMateInformation.jar" --sortorder "$sortOrder" </command><requirements><requirement type="package">picard</requirement></requirements><inputs> diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardGCBiasMetrics.xml --- a/tools/picard/rgPicardGCBiasMetrics.xml +++ b/tools/picard/rgPicardGCBiasMetrics.xml @@ -1,8 +1,8 @@ -<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02"> +<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="0.02.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" - -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectGcBiasMetrics.jar + -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectGcBiasMetrics.jar #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else: diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardHsMetrics.xml --- a/tools/picard/rgPicardHsMetrics.xml +++ b/tools/picard/rgPicardHsMetrics.xml @@ -1,10 +1,10 @@ -<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02"> +<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="0.02.1"><description>for targeted resequencing data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext" --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CalculateHsMetrics.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CalculateHsMetrics.jar" </command><requirements><requirement type="package">picard</requirement></requirements> diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardInsertSize.xml --- a/tools/picard/rgPicardInsertSize.xml +++ b/tools/picard/rgPicardInsertSize.xml @@ -1,10 +1,10 @@ -<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.0"> +<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.1"><description>for PAIRED data</description><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit" --histwidth "$histWidth" --minpct "$minPct" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" </command><inputs><param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardLibComplexity.xml --- a/tools/picard/rgPicardLibComplexity.xml +++ b/tools/picard/rgPicardLibComplexity.xml @@ -1,8 +1,8 @@ -<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01"> +<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file" </command><inputs><param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset" diff -r beb1986edd2838251441fcc47d7474ac1ed24d27 -r 18f2b18d48e845b49332c3fa7d6316cbadae15ef tools/picard/rgPicardMarkDups.xml --- a/tools/picard/rgPicardMarkDups.xml +++ b/tools/picard/rgPicardMarkDups.xml @@ -1,8 +1,8 @@ -<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01"> +<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01.1"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/MarkDuplicates.jar" -d "$html_file.files_path" -t "$html_file" -e "$input_file.ext" </command><requirements><requirement type="package">picard</requirement></requirements><inputs> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Minor cleanup in picard_SamToFastq.xml
by Bitbucket 25 Oct '11

25 Oct '11

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/beb1986edd28/ changeset: beb1986edd28 user: dan date: 2011-10-25 15:40:26 summary: Minor cleanup in picard_SamToFastq.xml affected #: 1 file diff -r 1b05c45a0c1ac22c4bac8c2f8685eae32ca67ce6 -r beb1986edd2838251441fcc47d7474ac1ed24d27 tools/picard/picard_SamToFastq.xml --- a/tools/picard/picard_SamToFastq.xml +++ b/tools/picard/picard_SamToFastq.xml @@ -39,7 +39,6 @@ #end if 2>&1 || echo "Error running SamToFastq" >&2 - ##&& echo "die die die" >&2 </command><inputs><param name="input_sam" type="data" format="sam" label="SAM file" /> @@ -85,6 +84,7 @@ <param name="read1_max_bases_to_write" value="" /><param name="re_reverse" value="True" /><param name="include_non_pf_reads" value="False" /> + <param name="clipping_action" value="" /><param name="clipping_attribute" value="" /><param name="include_non_primary_alignments" value="False" /><output name="output_fastq1" file="random_phiX_1.fastqsanger"/> @@ -99,6 +99,7 @@ <param name="read2_max_bases_to_write" value="" /><param name="re_reverse" value="True" /><param name="include_non_pf_reads" value="False" /> + <param name="clipping_action" value="" /><param name="clipping_attribute" value="" /><param name="include_non_primary_alignments" value="False" /><output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 24 Oct '11

24 Oct '11

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b1134c82e101/ changeset: b1134c82e101 user: jgoecks date: 2011-10-25 02:28:28 summary: Trackster: refactor constructor code for cleaner initialization. affected #: 1 file diff -r d0842bf94ff95b7b34cb46f5dbcc9a25167110c7 -r b1134c82e101b47545531f2318a9b060342c9fd2 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -2558,7 +2558,9 @@ predraw_init: function() {} }); -var TiledTrack = function(filters_list, tool_dict) { +var TiledTrack = function(name, view, container, show_header, prefs, filters_list, tool_dict, data_url, data_query_wait) { + Track.call(this, name, view, container, show_header, prefs, data_url, data_query_wait); + var track = this, view = track.view; @@ -2938,8 +2940,7 @@ }); var ReferenceTrack = function (view) { - Track.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {}); - TiledTrack.call(this); + TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, false, {}); view.reference_track = this; this.left_offset = 200; @@ -2991,8 +2992,7 @@ var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - Track.call( this, name, view, container, prefs ); - TiledTrack.call( this ); + TiledTrack.call( this, name, view, container, true, prefs ); this.min_height_px = 16; this.max_height_px = 400; @@ -3137,11 +3137,8 @@ // // Initialization. - // - - // FIXME: cleaner init needed; should just be able to call TiledTrack() - Track.call(this, name, view, container, true, prefs); - TiledTrack.call(this, filters, tool); + // + TiledTrack.call(this, name, view, container, true, prefs, filters, tool); // Define and restore track configuration. this.config = new DrawableConfig( { https://bitbucket.org/galaxy/galaxy-central/changeset/1b05c45a0c1a/ changeset: 1b05c45a0c1a user: jgoecks date: 2011-10-25 04:08:57 summary: Merge. affected #: 3 files diff -r b1134c82e101b47545531f2318a9b060342c9fd2 -r 1b05c45a0c1ac22c4bac8c2f8685eae32ca67ce6 tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -102,9 +102,9 @@ <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" /><param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" /><param name="ref_file" type="select" label="Using reference genome"> -  + <options from_data_table="picard_indexes"> +  + </options></param></when><when value="history"> diff -r b1134c82e101b47545531f2318a9b060342c9fd2 -r 1b05c45a0c1ac22c4bac8c2f8685eae32ca67ce6 tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -159,9 +159,9 @@ <param name="input_variant" type="data" format="vcf" label="Input variant file" /></repeat><param name="ref_file" type="select" label="Using reference genome"> -  + <options from_data_table="picard_indexes"> +  + </options></param></when><when value="history"> diff -r b1134c82e101b47545531f2318a9b060342c9fd2 -r 1b05c45a0c1ac22c4bac8c2f8685eae32ca67ce6 tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -152,9 +152,9 @@ <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" /></repeat><param name="ref_file" type="select" label="Using reference genome"> -  + <options from_data_table="picard_indexes"> +  + </options></param></when><when value="history"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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