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Requires Galaxy config change - merged former Galaxy config [datatypes] and [sniff order] sections, along with former datatype_converters.xml into 1 xml file, datatypes_conf.xml.
The new datatypes_conf.xml.sample should be copied to datatypes_conf.xml.
This commit is contained in:
Greg Von Kuster
@@ -1,11 +0,0 @@
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<?xml version="1.0"?>
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<converters>
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<converter file="bed_to_gff_converter.xml" source_datatype="bed" target_datatype="gff"/>
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<converter file="fasta_to_tabular_converter.xml" source_datatype="fasta" target_datatype="tabular"/>
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<converter file="fastq_to_fasta_converter.xml" source_datatype="fastqsolexa" target_datatype="fasta"/>
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<converter file="fastq_to_qual_converter.xml" source_datatype="fastqsolexa" target_datatype="qual"/>
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<converter file="gff_to_bed_converter.xml" source_datatype="gff" target_datatype="bed"/>
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<converter file="interval_to_bed_converter.xml" source_datatype="interval" target_datatype="bed"/>
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<converter file="maf_to_fasta_converter.xml" source_datatype="maf" target_datatype="fasta"/>
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<converter file="maf_to_interval_converter.xml" source_datatype="maf" target_datatype="interval"/>
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</converters>
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@@ -0,0 +1,163 @@
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<?xml version="1.0"?>
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<datatypes>
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<registration converters_path="lib/galaxy/datatypes/converters">
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<datatype extension="ab1" type="galaxy.datatypes.images:Ab1" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/>
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<datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true">
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<converter file="bed_to_gff_converter.xml" target_datatype="gff"/>
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</datatype>
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<datatype extension="binseq.zip" type="galaxy.datatypes.images:Binseq" mimetype="application/zip" display_in_upload="true"/>
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<datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
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<datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream"/>
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<datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true">
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<converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/>
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</datatype>
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<datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true">
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<converter file="fastq_to_fasta_converter.xml" target_datatype="fasta"/>
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<converter file="fastq_to_qual_converter.xml" target_datatype="qual"/>
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</datatype>
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<datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
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<converter file="gff_to_bed_converter.xml" target_datatype="bed"/>
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</datatype>
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<datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/>
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<datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/>
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<datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
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<datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
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<datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true">
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<converter file="interval_to_bed_converter.xml" target_datatype="bed"/>
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</datatype>
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<datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/>
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<datatype extension="laj" type="galaxy.datatypes.images:Laj"/>
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<datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/>
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<datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true">
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<converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/>
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<converter file="maf_to_interval_converter.xml" target_datatype="interval"/>
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</datatype>
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<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
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<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
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<datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" display_in_upload="true"/>
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<datatype extension="scf" type="galaxy.datatypes.images:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
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<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
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<datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
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<datatype extension="txtseq.zip" type="galaxy.datatypes.images:Txtseq" mimetype="application/zip" display_in_upload="true"/>
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<datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"/>
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<!-- EMBOSS TOOLS -->
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<datatype extension="acedb" type="galaxy.datatypes.data:Text"/>
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<datatype extension="asn1" type="galaxy.datatypes.data:Text"/>
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<datatype extension="btwisted" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cai" type="galaxy.datatypes.data:Text"/>
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<datatype extension="charge" type="galaxy.datatypes.data:Text"/>
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<datatype extension="checktrans" type="galaxy.datatypes.data:Text"/>
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<datatype extension="chips" type="galaxy.datatypes.data:Text"/>
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<datatype extension="clustal" type="galaxy.datatypes.data:Text"/>
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<datatype extension="codata" type="galaxy.datatypes.data:Text"/>
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<datatype extension="codcmp" type="galaxy.datatypes.data:Text"/>
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<datatype extension="coderet" type="galaxy.datatypes.data:Text"/>
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<datatype extension="compseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cpgplot" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cpgreport" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cusp" type="galaxy.datatypes.data:Text"/>
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<datatype extension="cut" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dan" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dbmotif" type="galaxy.datatypes.data:Text"/>
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<datatype extension="diffseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="digest" type="galaxy.datatypes.data:Text"/>
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<datatype extension="dreg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="einverted" type="galaxy.datatypes.data:Text"/>
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<datatype extension="embl" type="galaxy.datatypes.data:Text"/>
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<datatype extension="epestfind" type="galaxy.datatypes.data:Text"/>
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<datatype extension="equicktandem" type="galaxy.datatypes.data:Text"/>
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<datatype extension="est2genome" type="galaxy.datatypes.data:Text"/>
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<datatype extension="etandem" type="galaxy.datatypes.data:Text"/>
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<datatype extension="excel" type="galaxy.datatypes.data:Text"/>
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<datatype extension="feattable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fitch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="freak" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzznuc" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzzpro" type="galaxy.datatypes.data:Text"/>
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<datatype extension="fuzztran" type="galaxy.datatypes.data:Text"/>
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<datatype extension="garnier" type="galaxy.datatypes.data:Text"/>
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<datatype extension="gcg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="geecee" type="galaxy.datatypes.data:Text"/>
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<datatype extension="genbank" type="galaxy.datatypes.data:Text"/>
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<datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text"/>
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<datatype extension="hennig86" type="galaxy.datatypes.data:Text"/>
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<datatype extension="hmoment" type="galaxy.datatypes.data:Text"/>
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<datatype extension="ig" type="galaxy.datatypes.data:Text"/>
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<datatype extension="isochore" type="galaxy.datatypes.data:Text"/>
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<datatype extension="jackknifer" type="galaxy.datatypes.data:Text"/>
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<datatype extension="jackknifernon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx10" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx1" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx0" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx3" type="galaxy.datatypes.data:Text"/>
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<datatype extension="markx2" type="galaxy.datatypes.data:Text"/>
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<datatype extension="match" type="galaxy.datatypes.data:Text"/>
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<datatype extension="mega" type="galaxy.datatypes.data:Text"/>
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<datatype extension="meganon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="motif" type="galaxy.datatypes.data:Text"/>
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<datatype extension="msf" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nametable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="ncbi" type="galaxy.datatypes.data:Text"/>
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<datatype extension="needle" type="galaxy.datatypes.data:Text"/>
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<datatype extension="newcpgreport" type="galaxy.datatypes.data:Text"/>
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<datatype extension="newcpgseek" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nexus" type="galaxy.datatypes.data:Text"/>
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<datatype extension="nexusnon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="noreturn" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pair" type="galaxy.datatypes.data:Text"/>
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<datatype extension="palindrome" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepcoil" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepinfo" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pepstats" type="galaxy.datatypes.data:Text"/>
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<datatype extension="phylip" type="galaxy.datatypes.data:Text"/>
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<datatype extension="phylipnon" type="galaxy.datatypes.data:Text"/>
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<datatype extension="pir" type="galaxy.datatypes.data:Text"/>
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<datatype extension="polydot" type="galaxy.datatypes.data:Text"/>
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<datatype extension="preg" type="galaxy.datatypes.data:Text"/>
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<datatype extension="prettyseq" type="galaxy.datatypes.data:Text"/>
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<datatype extension="primersearch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="regions" type="galaxy.datatypes.data:Text"/>
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<datatype extension="score" type="galaxy.datatypes.data:Text"/>
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<datatype extension="selex" type="galaxy.datatypes.data:Text"/>
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<datatype extension="seqtable" type="galaxy.datatypes.data:Text"/>
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<datatype extension="showfeat" type="galaxy.datatypes.data:Text"/>
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<datatype extension="showorf" type="galaxy.datatypes.data:Text"/>
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<datatype extension="simple" type="galaxy.datatypes.data:Text"/>
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<datatype extension="sixpack" type="galaxy.datatypes.data:Text"/>
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<datatype extension="srs" type="galaxy.datatypes.data:Text"/>
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<datatype extension="srspair" type="galaxy.datatypes.data:Text"/>
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<datatype extension="staden" type="galaxy.datatypes.data:Text"/>
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<datatype extension="strider" type="galaxy.datatypes.data:Text"/>
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<datatype extension="supermatcher" type="galaxy.datatypes.data:Text"/>
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<datatype extension="swiss" type="galaxy.datatypes.data:Text"/>
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<datatype extension="syco" type="galaxy.datatypes.data:Text"/>
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<datatype extension="table" type="galaxy.datatypes.data:Text"/>
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<datatype extension="textsearch" type="galaxy.datatypes.data:Text"/>
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<datatype extension="vectorstrip" type="galaxy.datatypes.data:Text"/>
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<datatype extension="wobble" type="galaxy.datatypes.data:Text"/>
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<datatype extension="wordcount" type="galaxy.datatypes.data:Text"/>
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<datatype extension="tagseq" type="galaxy.datatypes.data:Text"/>
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</registration>
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<sniffers>
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<!--
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The order in which Galaxy attempts to determine data types is
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important because some formats are much more loosely defined
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than others.
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-->
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<sniffer order="05" type="galaxy.datatypes.sequence:Maf"/>
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<sniffer order="10" type="galaxy.datatypes.sequence:Lav"/>
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<sniffer order="15" type="galaxy.datatypes.sequence:Fasta"/>
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<sniffer order="20" type="galaxy.datatypes.sequence:Fastq"/>
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<sniffer order="25" type="galaxy.datatypes.sequence:FastqSolexa"/>
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<sniffer order="30" type="galaxy.datatypes.interval:Wiggle"/>
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<sniffer order="35" type="galaxy.datatypes.images:Html"/>
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<sniffer order="40" type="galaxy.datatypes.sequence:Axt"/>
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<sniffer order="45" type="galaxy.datatypes.interval:Bed"/>
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<sniffer order="50" type="galaxy.datatypes.interval:CustomTrack"/>
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<sniffer order="55" type="galaxy.datatypes.interval:Gff"/>
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<sniffer order="60" type="galaxy.datatypes.interval:Gff3"/>
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<sniffer order="65" type="galaxy.datatypes.interval:Interval"/>
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</sniffers>
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</datatypes>
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+4
-4
@@ -13,9 +13,9 @@ class UniverseApplication( object ):
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self.config = config.Configuration( **kwargs )
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self.config.check()
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config.configure_logging( self.config )
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#Set up datatypes registry
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self.datatypes_registry = galaxy.datatypes.registry.Registry(datatypes=self.config.datatypes, sniff_order=self.config.sniff_order)
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galaxy.model.set_datatypes_registry(self.datatypes_registry)
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# Set up datatypes registry
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self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config )
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galaxy.model.set_datatypes_registry( self.datatypes_registry )
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# Determine the database url
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if self.config.database_connection:
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db_url = self.config.database_connection
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@@ -29,7 +29,7 @@ class UniverseApplication( object ):
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# Initialize the tools
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self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self )
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#Load datatype converters
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self.datatypes_registry.load_datatype_converters(self.config.datatype_converters_config, self.config.datatype_converters_path, self.toolbox)
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self.datatypes_registry.load_datatype_converters( self.toolbox )
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# Start the job queue
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job_dispatcher = jobs.DefaultJobDispatcher( self )
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self.job_queue = jobs.JobQueue( self, job_dispatcher )
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+3
-14
@@ -72,27 +72,16 @@ class Configuration( object ):
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self.tool_runners = global_conf_parser.items("galaxy:tool_runners")
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except ConfigParser.NoSectionError:
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self.tool_runners = []
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#Store datatypes config
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try:
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self.datatypes = global_conf_parser.items("galaxy:datatypes")
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except ConfigParser.NoSectionError:
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self.datatypes = []
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#Store sniff order config
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try:
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self.sniff_order = global_conf_parser.items("galaxy:sniff_order")
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except ConfigParser.NoSectionError:
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self.sniff_order = []
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self.datatype_converters_config = kwargs.get( 'datatype_converters_config_file', "datatype_converters_conf.xml" )
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self.datatype_converters_path = kwargs.get( 'datatype_converters_path', os.path.join(self.root,"lib/galaxy/datatypes/converters") )
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self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
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def get( self, key, default ):
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return self.config_dict.get( key, default )
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def check( self ):
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# Check that required directories exist
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for path in self.root, self.file_path, self.tool_path, self.tool_data_path, self.template_path, self.job_working_directory, self.datatype_converters_path:
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for path in self.root, self.file_path, self.tool_path, self.tool_data_path, self.template_path, self.job_working_directory:
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if not os.path.isdir( path ):
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raise ConfigurationError("Directory does not exist: %s" % path )
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# Check that required files exist
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for path in self.tool_config, self.datatype_converters_config:
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for path in self.tool_config, self.datatypes_config:
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if not os.path.isfile(path):
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raise ConfigurationError("File not found: %s" % path )
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@@ -3,61 +3,92 @@ Provides mapping between extensions and datatypes, mime-types, etc.
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"""
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import os
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import logging
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import data, tabular, interval, images, sequence, qualityscore
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import genetics # needed for rgenetics tools
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import data, tabular, interval, images, sequence, qualityscore, genetics
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import galaxy.util
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from galaxy.util.odict import odict
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class ConfigurationError( Exception ):
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pass
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class Registry( object ):
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def __init__( self, datatypes=[], sniff_order=[] ):
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def __init__( self, root_dir=None, config=None ):
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self.log = logging.getLogger(__name__)
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self.datatypes_by_extension = {}
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self.mimetypes_by_extension = {}
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self.datatype_converters = odict()
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self.upload_file_formats = []
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self.converters = []
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self.sniff_order = []
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for ext, kind in datatypes:
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# Data types are defined in the config like this:
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# #<file extension> = <data type class>,<mime type (optional)>,<display in upload select list (optional)>
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try:
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fields = kind.split(",")
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kind = fields[0].strip()
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mime_type = None
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display_in_upload = False
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# See if we have a mime type or a display_in_upload
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self.upload_file_formats = []
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if root_dir and config:
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# Parse datatypes_conf.xml
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tree = galaxy.util.parse_xml( config )
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root = tree.getroot()
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# Load datatypes and converters from config
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self.log.debug( 'Loading datatypes from %s' % config )
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registration = root.find( 'registration' )
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self.datatype_converters_path = os.path.join( root_dir, registration.get( 'converters_path', 'lib/galaxy/datatypes/converters' ) )
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if not os.path.isdir( self.datatype_converters_path ):
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raise ConfigurationError( "Directory does not exist: %s" % self.datatype_converters_path )
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for elem in registration.findall( 'datatype' ):
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try:
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ele = fields[1].strip()
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if ele:
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if ele == 'display_in_upload':
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display_in_upload = True
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else:
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mime_type = ele
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except:
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pass
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# See if we have a display_in_upload
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if not display_in_upload:
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try:
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ele = fields[2].strip()
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if ele == 'display_in_upload':
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display_in_upload = True
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except:
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pass
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if display_in_upload:
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self.upload_file_formats.append( ext )
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fields = kind.split(":")
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datatype_module = fields[0]
|
||||
datatype_class = fields[1]
|
||||
fields = datatype_module.split(".")
|
||||
module = __import__( fields.pop(0) )
|
||||
for mod in fields:
|
||||
module = getattr(module,mod)
|
||||
self.datatypes_by_extension[ext] = getattr(module, datatype_class)()
|
||||
if mime_type is None:
|
||||
# Use default mime type as per datatype spec
|
||||
mime_type = self.datatypes_by_extension[ext].get_mime()
|
||||
self.mimetypes_by_extension[ext] = mime_type
|
||||
except Exception, e:
|
||||
self.log.warning('error loading datatype "%s", problem: %s' % ( ext, str( e ) ) )
|
||||
extension = elem.get( 'extension', None )
|
||||
type = elem.get( 'type', None )
|
||||
mimetype = elem.get( 'mimetype', None )
|
||||
display_in_upload = elem.get( 'display_in_upload', False )
|
||||
if extension and type:
|
||||
fields = type.split( ':' )
|
||||
datatype_module = fields[0]
|
||||
datatype_class = fields[1]
|
||||
fields = datatype_module.split( '.' )
|
||||
module = __import__( fields.pop(0) )
|
||||
for mod in fields:
|
||||
module = getattr( module, mod )
|
||||
self.datatypes_by_extension[extension] = getattr( module, datatype_class )()
|
||||
if mimetype is None:
|
||||
# Use default mime type as per datatype spec
|
||||
mimetype = self.datatypes_by_extension[extension].get_mime()
|
||||
self.mimetypes_by_extension[extension] = mimetype
|
||||
if display_in_upload:
|
||||
self.upload_file_formats.append( extension )
|
||||
for converter in elem.findall( 'converter' ):
|
||||
# Build the list of datatype converters which will later be loaded
|
||||
# into the calling app's toolbox.
|
||||
converter_config = converter.get( 'file', None )
|
||||
target_datatype = converter.get( 'target_datatype', None )
|
||||
if converter_config and target_datatype:
|
||||
self.converters.append( ( converter_config, extension, target_datatype ) )
|
||||
except Exception, e:
|
||||
self.log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) )
|
||||
# Load datatype sniffers from config
|
||||
sniff_order = []
|
||||
sniffers = root.find( 'sniffers' )
|
||||
for elem in sniffers.findall( 'sniffer' ):
|
||||
order = elem.get( 'order', None )
|
||||
type = elem.get( 'type', None )
|
||||
if order and type:
|
||||
sniff_order.append( ( order, type ) )
|
||||
sniff_order.sort()
|
||||
for ele in sniff_order:
|
||||
try:
|
||||
type = ele[1]
|
||||
fields = type.split( ":" )
|
||||
datatype_module = fields[0]
|
||||
datatype_class = fields[1]
|
||||
fields = datatype_module.split( "." )
|
||||
module = __import__( fields.pop(0) )
|
||||
for mod in fields:
|
||||
module = getattr( module, mod )
|
||||
aclass = getattr( module, datatype_class )()
|
||||
included = False
|
||||
for atype in self.sniff_order:
|
||||
if not issubclass( atype.__class__, aclass.__class__ ) and isinstance( atype, aclass.__class__ ):
|
||||
included = True
|
||||
break
|
||||
if not included:
|
||||
self.sniff_order.append( aclass )
|
||||
self.log.debug( 'Loaded sniffer for datatype: %s' % type )
|
||||
except Exception, exc:
|
||||
self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( type, str( exc ) ) )
|
||||
#default values
|
||||
if len(self.datatypes_by_extension) < 1:
|
||||
self.datatypes_by_extension = {
|
||||
@@ -104,33 +135,8 @@ class Registry( object ):
|
||||
'txtseq.zip' : 'application/zip',
|
||||
'wig' : 'text/plain'
|
||||
}
|
||||
"""
|
||||
The order in which we attempt to determine data types is critical
|
||||
because some formats are much more flexibly defined than others.
|
||||
"""
|
||||
sniff_order.sort()
|
||||
for ele in sniff_order:
|
||||
try:
|
||||
ord = ele[0]
|
||||
kind = ele[1]
|
||||
fields = kind.split( ":" )
|
||||
datatype_module = fields[0]
|
||||
datatype_class = fields[1]
|
||||
fields = datatype_module.split( "." )
|
||||
module = __import__( fields.pop(0) )
|
||||
for mod in fields:
|
||||
module = getattr( module, mod )
|
||||
aclass = getattr( module, datatype_class )()
|
||||
included = False
|
||||
for atype in self.sniff_order:
|
||||
if not issubclass( atype.__class__, aclass.__class__ ) and isinstance( atype, aclass.__class__ ):
|
||||
included = True
|
||||
break
|
||||
if not included:
|
||||
self.sniff_order.append( aclass )
|
||||
except Exception, exc:
|
||||
self.log.warning( 'error appending datatype: %s to sniff_order, error: %s' % ( str( kind ), str( exc ) ) )
|
||||
#default values
|
||||
# Default values - the order in which we attempt to determine data types is critical
|
||||
# because some formats are much more flexibly defined than others.
|
||||
if len(self.sniff_order) < 1:
|
||||
self.sniff_order = [
|
||||
sequence.Maf(),
|
||||
@@ -146,7 +152,7 @@ class Registry( object ):
|
||||
interval.Interval()
|
||||
]
|
||||
def append_to_sniff_order():
|
||||
"""Just in case any supported data types are not included in the config's sniff_order section."""
|
||||
# Just in case any supported data types are not included in the config's sniff_order section.
|
||||
for ext in self.datatypes_by_extension:
|
||||
datatype = self.datatypes_by_extension[ext]
|
||||
included = False
|
||||
@@ -157,7 +163,7 @@ class Registry( object ):
|
||||
if not included:
|
||||
self.sniff_order.append(datatype)
|
||||
append_to_sniff_order()
|
||||
|
||||
|
||||
def get_mimetype_by_extension(self, ext ):
|
||||
"""Returns a mimetype based on an extension"""
|
||||
try:
|
||||
@@ -196,24 +202,20 @@ class Registry( object ):
|
||||
setattr(newdata, key, value)
|
||||
newdata.ext = ext
|
||||
return newdata
|
||||
|
||||
def load_datatype_converters(self, datatype_converters_config, datatype_converters_path, toolbox):
|
||||
"""Loads datatype converters from a file, and adds to the toolbox"""
|
||||
self.datatype_converters = odict()
|
||||
tree = galaxy.util.parse_xml( datatype_converters_config )
|
||||
root = tree.getroot()
|
||||
self.log.debug( "Loading converters from %s" % (datatype_converters_config) )
|
||||
for elem in root.findall("converter"):
|
||||
path = elem.get("file")
|
||||
source_datatype = elem.get("source_datatype").split(",")
|
||||
target_datatype = elem.get("target_datatype")
|
||||
converter = toolbox.load_tool( os.path.join( datatype_converters_path, path ) )
|
||||
self.log.debug( "Loaded converter: %s", converter.id )
|
||||
|
||||
def load_datatype_converters( self, toolbox ):
|
||||
"""Adds datatype converters from self.converters to the calling app's toolbox"""
|
||||
for elem in self.converters:
|
||||
tool_config = elem[0]
|
||||
source_datatype = elem[1]
|
||||
target_datatype = elem[2]
|
||||
converter = toolbox.load_tool( os.path.join( self.datatype_converters_path, tool_config ) )
|
||||
toolbox.tools_by_id[converter.id] = converter
|
||||
for source_d in source_datatype:
|
||||
if source_d not in self.datatype_converters:
|
||||
self.datatype_converters[source_d] = odict()
|
||||
self.datatype_converters[source_d][target_datatype] = converter
|
||||
if source_datatype not in self.datatype_converters:
|
||||
self.datatype_converters[source_datatype] = odict()
|
||||
self.datatype_converters[source_datatype][target_datatype] = converter
|
||||
self.log.debug( "Loaded converter: %s", converter.id )
|
||||
|
||||
def get_converters_by_datatype(self, ext):
|
||||
"""Returns available converters by source type"""
|
||||
converters = odict()
|
||||
|
||||
+5
-152
@@ -92,7 +92,7 @@ use_new_layout = true
|
||||
|
||||
# Comma separated list of UCSC / gbrowse browsers to use for viewing
|
||||
ucsc_display_sites = main,test,archaea
|
||||
gbrowse_display_sites = wormbase,flybase,elegans
|
||||
gbrowse_display_sites = elegans,flybase
|
||||
|
||||
# Serving static files (needed if running standalone)
|
||||
static_enabled = True
|
||||
@@ -117,7 +117,7 @@ static_style_dir = %(here)s/static/june_2007_style/blue
|
||||
# ---- Job Runners ----------------------------------------------------------
|
||||
|
||||
# Clustering Galaxy is not a straightforward process and requires a lot of
|
||||
# pre-configuration. Please see the Galaxy Wiki before attempting to set any
|
||||
# pre-configuration. See the ClusteringGalaxy Wiki before attempting to set any
|
||||
# of these options. If running normally (without a cluster), do not change
|
||||
# anything in this section.
|
||||
|
||||
@@ -129,10 +129,11 @@ static_style_dir = %(here)s/static/june_2007_style/blue
|
||||
|
||||
# default_cluster_job_runner: The URL for the default runner to use when a tool
|
||||
# doesn't explicity define a runner below. For help on the cluster URL format,
|
||||
# see the Galaxy Wiki. Leave commented if not using a cluster job runner.
|
||||
# see the ClusteringGalaxy Wiki. Leave commented if not using a cluster job runner.
|
||||
#default_cluster_job_runner = pbs:///
|
||||
|
||||
# The PBS options are described in detail on the Galaxy Wiki
|
||||
# The PBS options are described in detail in the Galaxy Configuration section of
|
||||
# the ClusteringGalaxy Wiki
|
||||
#pbs_application_server =
|
||||
#pbs_stage_path =
|
||||
#pbs_dataset_server =
|
||||
@@ -162,151 +163,3 @@ ucsc_table_direct1 = local:///
|
||||
ucsc_table_direct_archaea1 = local:///
|
||||
ucsc_table_direct_test1 = local:///
|
||||
upload1 = local:///
|
||||
|
||||
# ---- Datatypes ------------------------------------------------------------
|
||||
|
||||
[galaxy:datatypes]
|
||||
|
||||
#<file extension> = <data type class>,<mime type (optional)>,<display in upload select list (optional)>
|
||||
ab1 = galaxy.datatypes.images:Ab1,application/octet-stream,display_in_upload
|
||||
axt = galaxy.datatypes.sequence:Axt,display_in_upload
|
||||
bed = galaxy.datatypes.interval:Bed,display_in_upload
|
||||
binseq.zip = galaxy.datatypes.images:Binseq,application/zip,display_in_upload
|
||||
customtrack = galaxy.datatypes.interval:CustomTrack
|
||||
data = galaxy.datatypes.data:Data,application/octet-stream
|
||||
fasta = galaxy.datatypes.sequence:Fasta,display_in_upload
|
||||
fastqsolexa = galaxy.datatypes.sequence:FastqSolexa,display_in_upload
|
||||
gff = galaxy.datatypes.interval:Gff,display_in_upload
|
||||
gff3 = galaxy.datatypes.interval:Gff3,display_in_upload
|
||||
gif = galaxy.datatypes.images:Image,image/gif
|
||||
gmaj.zip = galaxy.datatypes.images:Gmaj,application/zip
|
||||
html = galaxy.datatypes.images:Html,text/html
|
||||
interval = galaxy.datatypes.interval:Interval,display_in_upload
|
||||
jpg = galaxy.datatypes.images:Image,image/jpeg
|
||||
laj = galaxy.datatypes.images:Laj
|
||||
lav = galaxy.datatypes.sequence:Lav,display_in_upload
|
||||
maf = galaxy.datatypes.sequence:Maf,display_in_upload
|
||||
pdf = galaxy.datatypes.images:Image,application/pdf
|
||||
png = galaxy.datatypes.images:Image,image/png
|
||||
qual = galaxy.datatypes.qualityscore:QualityScore,display_in_upload
|
||||
scf = galaxy.datatypes.images:Scf,application/octet-stream,display_in_upload
|
||||
taxonomy = galaxy.datatypes.tabular:Taxonomy,display_in_upload
|
||||
tabular = galaxy.datatypes.tabular:Tabular,display_in_upload
|
||||
txt = galaxy.datatypes.data:Text,display_in_upload
|
||||
txtseq.zip = galaxy.datatypes.images:Txtseq,application/zip,display_in_upload
|
||||
wig = galaxy.datatypes.interval:Wiggle,display_in_upload
|
||||
#EMBOSS TOOLS
|
||||
acedb = galaxy.datatypes.data:Text
|
||||
asn1 = galaxy.datatypes.data:Text
|
||||
btwisted = galaxy.datatypes.data:Text
|
||||
cai = galaxy.datatypes.data:Text
|
||||
charge = galaxy.datatypes.data:Text
|
||||
checktrans = galaxy.datatypes.data:Text
|
||||
chips = galaxy.datatypes.data:Text
|
||||
clustal = galaxy.datatypes.data:Text
|
||||
codata = galaxy.datatypes.data:Text
|
||||
codcmp = galaxy.datatypes.data:Text
|
||||
coderet = galaxy.datatypes.data:Text
|
||||
compseq = galaxy.datatypes.data:Text
|
||||
cpgplot = galaxy.datatypes.data:Text
|
||||
cpgreport = galaxy.datatypes.data:Text
|
||||
cusp = galaxy.datatypes.data:Text
|
||||
cut = galaxy.datatypes.data:Text
|
||||
dan = galaxy.datatypes.data:Text
|
||||
dbmotif = galaxy.datatypes.data:Text
|
||||
diffseq = galaxy.datatypes.data:Text
|
||||
digest = galaxy.datatypes.data:Text
|
||||
dreg = galaxy.datatypes.data:Text
|
||||
einverted = galaxy.datatypes.data:Text
|
||||
embl = galaxy.datatypes.data:Text
|
||||
epestfind = galaxy.datatypes.data:Text
|
||||
equicktandem = galaxy.datatypes.data:Text
|
||||
est2genome = galaxy.datatypes.data:Text
|
||||
etandem = galaxy.datatypes.data:Text
|
||||
excel = galaxy.datatypes.data:Text
|
||||
feattable = galaxy.datatypes.data:Text
|
||||
fitch = galaxy.datatypes.data:Text
|
||||
freak = galaxy.datatypes.data:Text
|
||||
fuzznuc = galaxy.datatypes.data:Text
|
||||
fuzzpro = galaxy.datatypes.data:Text
|
||||
fuzztran = galaxy.datatypes.data:Text
|
||||
garnier = galaxy.datatypes.data:Text
|
||||
gcg = galaxy.datatypes.data:Text
|
||||
geecee = galaxy.datatypes.data:Text
|
||||
genbank = galaxy.datatypes.data:Text
|
||||
helixturnhelix = galaxy.datatypes.data:Text
|
||||
hennig86 = galaxy.datatypes.data:Text
|
||||
hmoment = galaxy.datatypes.data:Text
|
||||
ig = galaxy.datatypes.data:Text
|
||||
isochore = galaxy.datatypes.data:Text
|
||||
jackknifer = galaxy.datatypes.data:Text
|
||||
jackknifernon = galaxy.datatypes.data:Text
|
||||
markx10 = galaxy.datatypes.data:Text
|
||||
markx1 = galaxy.datatypes.data:Text
|
||||
markx0 = galaxy.datatypes.data:Text
|
||||
markx3 = galaxy.datatypes.data:Text
|
||||
markx2 = galaxy.datatypes.data:Text
|
||||
match = galaxy.datatypes.data:Text
|
||||
mega = galaxy.datatypes.data:Text
|
||||
meganon = galaxy.datatypes.data:Text
|
||||
motif = galaxy.datatypes.data:Text
|
||||
msf = galaxy.datatypes.data:Text
|
||||
nametable = galaxy.datatypes.data:Text
|
||||
ncbi = galaxy.datatypes.data:Text
|
||||
needle = galaxy.datatypes.data:Text
|
||||
newcpgreport = galaxy.datatypes.data:Text
|
||||
newcpgseek = galaxy.datatypes.data:Text
|
||||
nexus = galaxy.datatypes.data:Text
|
||||
nexusnon = galaxy.datatypes.data:Text
|
||||
noreturn = galaxy.datatypes.data:Text
|
||||
pair = galaxy.datatypes.data:Text
|
||||
palindrome = galaxy.datatypes.data:Text
|
||||
pepcoil = galaxy.datatypes.data:Text
|
||||
pepinfo = galaxy.datatypes.data:Text
|
||||
pepstats = galaxy.datatypes.data:Text
|
||||
phylip = galaxy.datatypes.data:Text
|
||||
phylipnon = galaxy.datatypes.data:Text
|
||||
pir = galaxy.datatypes.data:Text
|
||||
polydot = galaxy.datatypes.data:Text
|
||||
preg = galaxy.datatypes.data:Text
|
||||
prettyseq = galaxy.datatypes.data:Text
|
||||
primersearch = galaxy.datatypes.data:Text
|
||||
regions = galaxy.datatypes.data:Text
|
||||
score = galaxy.datatypes.data:Text
|
||||
selex = galaxy.datatypes.data:Text
|
||||
seqtable = galaxy.datatypes.data:Text
|
||||
showfeat = galaxy.datatypes.data:Text
|
||||
showorf = galaxy.datatypes.data:Text
|
||||
simple = galaxy.datatypes.data:Text
|
||||
sixpack = galaxy.datatypes.data:Text
|
||||
srs = galaxy.datatypes.data:Text
|
||||
srspair = galaxy.datatypes.data:Text
|
||||
staden = galaxy.datatypes.data:Text
|
||||
strider = galaxy.datatypes.data:Text
|
||||
supermatcher = galaxy.datatypes.data:Text
|
||||
swiss = galaxy.datatypes.data:Text
|
||||
syco = galaxy.datatypes.data:Text
|
||||
table = galaxy.datatypes.data:Text
|
||||
textsearch = galaxy.datatypes.data:Text
|
||||
vectorstrip = galaxy.datatypes.data:Text
|
||||
wobble = galaxy.datatypes.data:Text
|
||||
wordcount = galaxy.datatypes.data:Text
|
||||
tagseq = galaxy.datatypes.data:Text
|
||||
|
||||
# ---- Data Type Sniff Order --------------------------------------------------
|
||||
|
||||
[galaxy:sniff_order]
|
||||
|
||||
05 = galaxy.datatypes.sequence:Maf
|
||||
10 = galaxy.datatypes.sequence:Lav
|
||||
15 = galaxy.datatypes.sequence:Fasta
|
||||
20 = galaxy.datatypes.sequence:Fastq
|
||||
25 = galaxy.datatypes.sequence:FastqSolexa
|
||||
30 = galaxy.datatypes.interval:Wiggle
|
||||
35 = galaxy.datatypes.images:Html
|
||||
40 = galaxy.datatypes.sequence:Axt
|
||||
45 = galaxy.datatypes.interval:Bed
|
||||
50 = galaxy.datatypes.interval:CustomTrack
|
||||
55 = galaxy.datatypes.interval:Gff
|
||||
60 = galaxy.datatypes.interval:Gff3
|
||||
65 = galaxy.datatypes.interval:Interval
|
||||
|
||||
Reference in New Issue
Block a user