Move tools, images, and templates in to lib/galaxy/ for inclusion in

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wheels and packages.

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Nate Coraor

2016-07-07 13:49:27 -04:00

parent cfc3bee2a2

commit 77c2d15361

805 changed files with 2 additions and 0 deletions

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display_applications/biom/biom_simple.xml → lib/galaxy/datatypes/display_applications/configs/biom/biom_simple.xml

display_applications/ensembl/ensembl_bam.xml → lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_bam.xml

display_applications/ensembl/ensembl_gff.xml → lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_gff.xml

display_applications/ensembl/ensembl_interval_as_bed.xml → lib/galaxy/datatypes/display_applications/configs/ensembl/ensembl_interval_as_bed.xml

display_applications/gbrowse/gbrowse_gff.xml → lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_gff.xml

display_applications/gbrowse/gbrowse_interval_as_bed.xml → lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_interval_as_bed.xml

display_applications/gbrowse/gbrowse_wig.xml → lib/galaxy/datatypes/display_applications/configs/gbrowse/gbrowse_wig.xml

display_applications/igb/bam.xml → lib/galaxy/datatypes/display_applications/configs/igb/bam.xml

display_applications/igb/bb.xml → lib/galaxy/datatypes/display_applications/configs/igb/bb.xml

display_applications/igb/bed.xml → lib/galaxy/datatypes/display_applications/configs/igb/bed.xml

display_applications/igb/bedgraph.xml → lib/galaxy/datatypes/display_applications/configs/igb/bedgraph.xml

display_applications/igb/bigwig.xml → lib/galaxy/datatypes/display_applications/configs/igb/bigwig.xml

display_applications/igb/gtf.xml → lib/galaxy/datatypes/display_applications/configs/igb/gtf.xml

display_applications/igb/wig.xml → lib/galaxy/datatypes/display_applications/configs/igb/wig.xml

display_applications/igv/bam.xml → lib/galaxy/datatypes/display_applications/configs/igv/bam.xml

display_applications/igv/gff.xml → lib/galaxy/datatypes/display_applications/configs/igv/gff.xml

display_applications/igv/interval_as_bed.xml → lib/galaxy/datatypes/display_applications/configs/igv/interval_as_bed.xml

display_applications/igv/vcf.xml → lib/galaxy/datatypes/display_applications/configs/igv/vcf.xml

display_applications/iobio/bam.xml → lib/galaxy/datatypes/display_applications/configs/iobio/bam.xml

display_applications/iobio/vcf.xml → lib/galaxy/datatypes/display_applications/configs/iobio/vcf.xml

display_applications/rviewer/bed.xml → lib/galaxy/datatypes/display_applications/configs/rviewer/bed.xml

display_applications/rviewer/vcf.xml → lib/galaxy/datatypes/display_applications/configs/rviewer/vcf.xml

display_applications/ucsc/bam.xml → lib/galaxy/datatypes/display_applications/configs/ucsc/bam.xml

display_applications/ucsc/bigbed.xml → lib/galaxy/datatypes/display_applications/configs/ucsc/bigbed.xml

display_applications/ucsc/bigwig.xml → lib/galaxy/datatypes/display_applications/configs/ucsc/bigwig.xml

display_applications/ucsc/interval_as_bed.xml → lib/galaxy/datatypes/display_applications/configs/ucsc/interval_as_bed.xml

display_applications/ucsc/maf_customtrack.xml → lib/galaxy/datatypes/display_applications/configs/ucsc/maf_customtrack.xml

display_applications/ucsc/vcf.xml → lib/galaxy/datatypes/display_applications/configs/ucsc/vcf.xml

tools/data_source/access_libraries.xml → lib/galaxy/tools/bundled/data_source/access_libraries.xml

tools/data_source/bed_convert.xml → lib/galaxy/tools/bundled/data_source/bed_convert.xml

tools/data_source/biomart.xml → lib/galaxy/tools/bundled/data_source/biomart.xml

tools/data_source/biomart_test.xml → lib/galaxy/tools/bundled/data_source/biomart_test.xml

tools/data_source/cbi_rice_mart.xml → lib/galaxy/tools/bundled/data_source/cbi_rice_mart.xml

tools/data_source/data_source.py → lib/galaxy/tools/bundled/data_source/data_source.py

tools/data_source/ebi_sra.xml → lib/galaxy/tools/bundled/data_source/ebi_sra.xml

tools/data_source/eupathdb.xml → lib/galaxy/tools/bundled/data_source/eupathdb.xml

tools/data_source/fetch.py → lib/galaxy/tools/bundled/data_source/fetch.py

tools/data_source/fly_modencode.xml → lib/galaxy/tools/bundled/data_source/fly_modencode.xml

tools/data_source/flymine.xml → lib/galaxy/tools/bundled/data_source/flymine.xml

tools/data_source/flymine_test.xml → lib/galaxy/tools/bundled/data_source/flymine_test.xml

tools/data_source/genbank.py → lib/galaxy/tools/bundled/data_source/genbank.py

tools/data_source/genbank.xml → lib/galaxy/tools/bundled/data_source/genbank.xml

tools/data_source/gramene_mart.xml → lib/galaxy/tools/bundled/data_source/gramene_mart.xml

tools/data_source/hapmapmart.xml → lib/galaxy/tools/bundled/data_source/hapmapmart.xml

tools/data_source/hbvar.xml → lib/galaxy/tools/bundled/data_source/hbvar.xml

tools/data_source/hbvar_filter.py → lib/galaxy/tools/bundled/data_source/hbvar_filter.py

tools/data_source/import.py → lib/galaxy/tools/bundled/data_source/import.py

tools/data_source/import.xml → lib/galaxy/tools/bundled/data_source/import.xml

tools/data_source/metabolicmine.xml → lib/galaxy/tools/bundled/data_source/metabolicmine.xml

tools/data_source/microbial_import.py → lib/galaxy/tools/bundled/data_source/microbial_import.py

tools/data_source/microbial_import.xml → lib/galaxy/tools/bundled/data_source/microbial_import.xml

tools/data_source/microbial_import_code.py → lib/galaxy/tools/bundled/data_source/microbial_import_code.py

tools/data_source/modmine.xml → lib/galaxy/tools/bundled/data_source/modmine.xml

tools/data_source/mousemine.xml → lib/galaxy/tools/bundled/data_source/mousemine.xml

tools/data_source/ratmine.xml → lib/galaxy/tools/bundled/data_source/ratmine.xml

tools/data_source/ucsc_tablebrowser.xml → lib/galaxy/tools/bundled/data_source/ucsc_tablebrowser.xml

tools/data_source/ucsc_tablebrowser_archaea.xml → lib/galaxy/tools/bundled/data_source/ucsc_tablebrowser_archaea.xml

tools/data_source/ucsc_tablebrowser_test.xml → lib/galaxy/tools/bundled/data_source/ucsc_tablebrowser_test.xml

tools/data_source/upload.py → lib/galaxy/tools/bundled/data_source/upload.py

tools/data_source/upload.xml → lib/galaxy/tools/bundled/data_source/upload.xml

tools/data_source/worm_modencode.xml → lib/galaxy/tools/bundled/data_source/worm_modencode.xml

tools/data_source/wormbase.xml → lib/galaxy/tools/bundled/data_source/wormbase.xml

tools/data_source/wormbase_test.xml → lib/galaxy/tools/bundled/data_source/wormbase_test.xml

tools/data_source/yeastmine.xml → lib/galaxy/tools/bundled/data_source/yeastmine.xml

tools/data_source/zebrafishmine.xml → lib/galaxy/tools/bundled/data_source/zebrafishmine.xml

tools/evolution/add_scores.py → lib/galaxy/tools/bundled/evolution/add_scores.py

tools/evolution/add_scores.xml → lib/galaxy/tools/bundled/evolution/add_scores.xml

tools/evolution/codingSnps.pl → lib/galaxy/tools/bundled/evolution/codingSnps.pl

tools/evolution/codingSnps.xml → lib/galaxy/tools/bundled/evolution/codingSnps.xml

tools/evolution/codingSnps_filter.py → lib/galaxy/tools/bundled/evolution/codingSnps_filter.py

tools/extract/extract_genomic_dna.py → lib/galaxy/tools/bundled/extract/extract_genomic_dna.py

tools/extract/extract_genomic_dna.xml → lib/galaxy/tools/bundled/extract/extract_genomic_dna.xml

tools/extract/liftOver_wrapper.py → lib/galaxy/tools/bundled/extract/liftOver_wrapper.py

tools/extract/liftOver_wrapper.xml → lib/galaxy/tools/bundled/extract/liftOver_wrapper.xml

tools/filters/CreateInterval.pl → lib/galaxy/tools/bundled/filters/CreateInterval.pl

tools/filters/CreateInterval.xml → lib/galaxy/tools/bundled/filters/CreateInterval.xml

tools/filters/axt_to_concat_fasta.py → lib/galaxy/tools/bundled/filters/axt_to_concat_fasta.py

tools/filters/axt_to_concat_fasta.xml → lib/galaxy/tools/bundled/filters/axt_to_concat_fasta.xml

tools/filters/axt_to_fasta.py → lib/galaxy/tools/bundled/filters/axt_to_fasta.py

tools/filters/axt_to_fasta.xml → lib/galaxy/tools/bundled/filters/axt_to_fasta.xml

tools/filters/axt_to_lav.py → lib/galaxy/tools/bundled/filters/axt_to_lav.py

tools/filters/axt_to_lav.xml → lib/galaxy/tools/bundled/filters/axt_to_lav.xml

tools/filters/axt_to_lav_code.py → lib/galaxy/tools/bundled/filters/axt_to_lav_code.py

tools/filters/bed2gff.xml → lib/galaxy/tools/bundled/filters/bed2gff.xml

tools/filters/bed_to_bigbed.xml → lib/galaxy/tools/bundled/filters/bed_to_bigbed.xml

tools/filters/bed_to_gff_converter.py → lib/galaxy/tools/bundled/filters/bed_to_gff_converter.py

tools/filters/catWrapper.py → lib/galaxy/tools/bundled/filters/catWrapper.py

tools/filters/catWrapper.xml → lib/galaxy/tools/bundled/filters/catWrapper.xml

tools/filters/changeCase.pl → lib/galaxy/tools/bundled/filters/changeCase.pl

tools/filters/changeCase.xml → lib/galaxy/tools/bundled/filters/changeCase.xml

tools/filters/commWrapper.pl → lib/galaxy/tools/bundled/filters/commWrapper.pl

tools/filters/commWrapper.xml → lib/galaxy/tools/bundled/filters/commWrapper.xml

tools/filters/compare.xml → lib/galaxy/tools/bundled/filters/compare.xml

tools/filters/condense_characters.pl → lib/galaxy/tools/bundled/filters/condense_characters.pl

tools/filters/condense_characters.xml → lib/galaxy/tools/bundled/filters/condense_characters.xml

tools/filters/convert_characters.pl → lib/galaxy/tools/bundled/filters/convert_characters.pl

tools/filters/convert_characters.py → lib/galaxy/tools/bundled/filters/convert_characters.py

tools/filters/convert_characters.xml → lib/galaxy/tools/bundled/filters/convert_characters.xml

tools/filters/cutWrapper.pl → lib/galaxy/tools/bundled/filters/cutWrapper.pl

tools/filters/cutWrapper.xml → lib/galaxy/tools/bundled/filters/cutWrapper.xml

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