From 695aa8f44dabbd6a00c8410ee7fdbff671c01a98 Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Tue, 1 Oct 2013 13:54:57 -0400 Subject: [PATCH] Migrate cuffcompare, cuffdiff, cufflinks, and cuffmerge from the distribution to the tool shed. Update the 'Review migration stages' layout. --- .../migrate/versions/0008_tools.py | 164 ++++++------ scripts/migrate_tools/0008_tools.xml | 12 + .../admin/review_tool_migration_stages.mako | 3 +- tool_conf.xml.sample | 190 +++++++++----- tools/ngs_rna/cuffcompare_wrapper.py | 138 ---------- tools/ngs_rna/cuffcompare_wrapper.xml | 223 ---------------- tools/ngs_rna/cuffdiff_wrapper.xml | 246 ------------------ tools/ngs_rna/cufflinks_wrapper.py | 227 ---------------- tools/ngs_rna/cufflinks_wrapper.xml | 235 ----------------- tools/ngs_rna/cuffmerge_wrapper.py | 138 ---------- tools/ngs_rna/cuffmerge_wrapper.xml | 129 --------- 11 files changed, 219 insertions(+), 1486 deletions(-) delete mode 100644 tools/ngs_rna/cuffcompare_wrapper.py delete mode 100644 tools/ngs_rna/cuffcompare_wrapper.xml delete mode 100644 tools/ngs_rna/cuffdiff_wrapper.xml delete mode 100644 tools/ngs_rna/cufflinks_wrapper.py delete mode 100644 tools/ngs_rna/cufflinks_wrapper.xml delete mode 100644 tools/ngs_rna/cuffmerge_wrapper.py delete mode 100644 tools/ngs_rna/cuffmerge_wrapper.xml diff --git a/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py b/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py index e028d455afa..c822e136ad6 100644 --- a/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py +++ b/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py @@ -6,45 +6,49 @@ The following tools have been eliminated from the distribution: 3: Compute Motif Frequencies For All Motifs motif by motif 4: Compute Motif Frequencies in indel flanking regions 5: CTD analysis of chemicals, diseases, or genes -6: Delete Overlapping Indels from a chromosome indels file -7: Separate pgSnp alleles into columns -8: Draw Stacked Bar Plots for different categories and different criteria -9: Length Distribution chart -10: FASTA Width formatter -11: RNA/DNA converter -12: Draw quality score boxplot -13: Quality format converter (ASCII-Numeric) -14: Filter by quality -15: FASTQ to FASTA converter -16: Remove sequencing artifacts -17: Barcode Splitter -18: Clip adapter sequences -19: Collapse sequences -20: Draw nucleotides distribution chart -21: Compute quality statistics -22: Rename sequences -23: Reverse- Complement -24: Trim sequences -25: FunDO human genes associated with disease terms -26: HVIS visualization of genomic data with the Hilbert curve -27: Fetch Indels from 3-way alignments -28: Identify microsatellite births and deaths -29: Extract orthologous microsatellites for multiple (>2) species alignments -30: Mutate Codons with SNPs -31: Pileup-to-Interval condenses pileup format into ranges of bases -32: Filter pileup on coverage and SNPs -33: Filter SAM on bitwise flag values -34: Merge BAM Files merges BAM files together -35: Generate pileup from BAM dataset -36: SAM-to-BAM converts SAM format to BAM format -37: Convert SAM to interval -38: flagstat provides simple stats on BAM files -39: MPileup SNP and indel caller -40: rmdup remove PCR duplicates -41: Slice BAM by provided regions -42: Split paired end reads -43: T Test for Two Samples -44: Plotting tool for multiple series and graph types. +6: Cuffcompare +7: Cuffdiff +8: Cufflinks +9: Cuffmerge +10: Delete Overlapping Indels from a chromosome indels file +11: Separate pgSnp alleles into columns +12: Draw Stacked Bar Plots for different categories and different criteria +13: Length Distribution chart +14: FASTA Width formatter +15: RNA/DNA converter +16: Draw quality score boxplot +17: Quality format converter (ASCII-Numeric) +18: Filter by quality +19: FASTQ to FASTA converter +20: Remove sequencing artifacts +21: Barcode Splitter +22: Clip adapter sequences +23: Collapse sequences +24: Draw nucleotides distribution chart +25: Compute quality statistics +26: Rename sequences +27: Reverse- Complement +28: Trim sequences +29: FunDO human genes associated with disease terms +30: HVIS visualization of genomic data with the Hilbert curve +31: Fetch Indels from 3-way alignments +32: Identify microsatellite births and deaths +33: Extract orthologous microsatellites for multiple (>2) species alignments +34: Mutate Codons with SNPs +35: Pileup-to-Interval condenses pileup format into ranges of bases +36: Filter pileup on coverage and SNPs +37: Filter SAM on bitwise flag values +38: Merge BAM Files merges BAM files together +39: Generate pileup from BAM dataset +40: SAM-to-BAM converts SAM format to BAM format +41: Convert SAM to interval +42: flagstat provides simple stats on BAM files +43: MPileup SNP and indel caller +44: rmdup remove PCR duplicates +45: Slice BAM by provided regions +46: Split paired end reads +47: T Test for Two Samples +48: Plotting tool for multiple series and graph types. The tools are now available in the repositories respectively: @@ -53,45 +57,49 @@ The tools are now available in the repositories respectively: 3: compute_motif_frequencies_for_all_motifs 4: compute_motifs_frequency 5: ctd_batch -6: delete_overlapping_indels -7: divide_pg_snp -8: draw_stacked_barplots -9: fasta_clipping_histogram -10: fasta_formatter -11: fasta_nucleotide_changer -12: fastq_quality_boxplot -13: fastq_quality_converter -14: fastq_quality_filter -15: fastq_to_fasta -16: fastx_artifacts_filter -17: fastx_barcode_splitter -18: fastx_clipper -19: fastx_collapser -20: fastx_nucleotides_distribution -21: fastx_quality_statistics -22: fastx_renamer -23: fastx_reverse_complement -24: fastx_trimmer -25: hgv_fundo -26: hgv_hilbertvis -27: indels_3way -28: microsatellite_birthdeath -29: multispecies_orthologous_microsats -30: mutate_snp_codon -31: pileup_interval -32: pileup_parser -33: sam_bitwise_flag_filter -34: sam_merge -35: sam_pileup -36: sam_to_bam -37: sam2interval -38: samtools_flagstat -39: samtools_mpileup -40: samtools_rmdup -41: samtools_slice_bam -42: split_paired_reads -43: t_test_two_samples -44: xy_plot +6: cuffcompare +7: cuffdiff +8: cufflinks +9: cuffmerge +10: delete_overlapping_indels +11: divide_pg_snp +12: draw_stacked_barplots +13: fasta_clipping_histogram +14: fasta_formatter +15: fasta_nucleotide_changer +16: fastq_quality_boxplot +17: fastq_quality_converter +18: fastq_quality_filter +19: fastq_to_fasta +20: fastx_artifacts_filter +21: fastx_barcode_splitter +22: fastx_clipper +23: fastx_collapser +24: fastx_nucleotides_distribution +25: fastx_quality_statistics +26: fastx_renamer +27: fastx_reverse_complement +28: fastx_trimmer +29: hgv_fundo +30: hgv_hilbertvis +31: indels_3way +32: microsatellite_birthdeath +33: multispecies_orthologous_microsats +34: mutate_snp_codon +35: pileup_interval +36: pileup_parser +37: sam_bitwise_flag_filter +38: sam_merge +39: sam_pileup +40: sam_to_bam +41: sam2interval +42: samtools_flagstat +43: samtools_mpileup +44: samtools_rmdup +45: samtools_slice_bam +46: split_paired_reads +47: t_test_two_samples +48: xy_plot from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the diff --git a/scripts/migrate_tools/0008_tools.xml b/scripts/migrate_tools/0008_tools.xml index 339f1b3efbf..dca874a3149 100644 --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -15,6 +15,18 @@ + + + + + + + + + + + + diff --git a/templates/admin/review_tool_migration_stages.mako b/templates/admin/review_tool_migration_stages.mako index 2d520a06fe6..098a3774c27 100644 --- a/templates/admin/review_tool_migration_stages.mako +++ b/templates/admin/review_tool_migration_stages.mako @@ -35,6 +35,7 @@

+ <% from tool_shed.util.shed_util_common import to_html_string %> %for stage in migration_stages_dict.keys(): <% migration_command = 'sh ./scripts/migrate_tools/%04d_tools.sh' % stage @@ -54,7 +55,7 @@
-

${migration_info} Run commands from the Galaxy installation directory!

+

${to_html_string(migration_info)} Run commands from the Galaxy installation directory!

%if tool_dependencies: This migration stage includes tools that have tool dependencies that can be automatically installed. To install them, run:
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample index 6904231f887..623e71abefd 100644 --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -1,12 +1,12 @@ - + -

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