Skip to content

Commit

Permalink
update Main's tools
Browse files Browse the repository at this point in the history 
* remove all of anton's vcflib tools (were hidden)
* remove all versions of vcffilter
* update bamtools
* update Deseq2
* update bowtie2
* update samtool_filter2
* update xy_plot
* update sra_tools
* update fastq_paired_end
* install star_fusion
* update stringtie
* update featurecounts
* update bwa
  • Loading branch information
@martenson
martenson committed Mar 23, 2018
1 parent 21d22b4 commit 34a4dd4
Show file tree
Hide file tree
Showing 3 changed files with 235 additions and 288 deletions.
36 changes: 12 additions & 24 deletions env/main/files/galaxy/var/integrated_tool_panel.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -162,6 +162,8 @@
<tool id="Extract genomic DNA 1" />
</section>
<section id="cshl_library_information" name="NGS: QC and manipulation" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.3.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.2" />
Expand Down Expand Up @@ -307,6 +309,10 @@
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.2.0" />
</section>
<section id="ngs_mapping" name="NGS: Mapping" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/star_fusion/star_fusion/0.5.4-3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.2.2" />
Expand Down Expand Up @@ -335,6 +341,9 @@
<label id="ab_solid" text="AB-SOLiD" version="" />
</section>
<section id="ngs-rna-tools" name="NGS: RNA Analysis" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.1.0" />
Expand Down Expand Up @@ -442,6 +451,7 @@
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.3" />
</section>
<section id="ngs:_bam_tools" name="NGS: BamTools" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.4.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.4.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2" />
Expand Down Expand Up @@ -560,14 +570,11 @@
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfprimers/vcfprimers/1.0.0_rc1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfleftalign/vcfleftalign/1.0.0_rc1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfselectsamples/vcfselectsamples/1.0.0_rc1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/1.0.0_rc1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfvcfintersect/vcfvcfintersect/1.0.0_rc1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcffixup/vcffixup/1.0.0_rc1.0" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/0.0.4" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfgeno2haplo/vcfgeno2haplo/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfcombine/vcfcombine/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcffilter/vcffilter2/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcf2tsv/vcf2tsv/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfallelicprimitives/vcfallelicprimitives/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfbreakcreatemulti/vcfbreakcreatemulti/0.0.3" />
Expand All @@ -588,27 +595,6 @@
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfdistance/vcfdistance/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfcommonsamples/vcfcommonsamples/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/vcfannotate/vcfannotate/0.0.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcffixup/vcffixup/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfprimers/vcfprimers/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfcombine/vcfcombine/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfbreakcreatemulti/vcfbreakcreatemulti/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfallelicprimitives/vcfallelicprimitives/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcffilter/vcffilter/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfrandomsample/vcfrandomsample/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfgeno2haplo/vcfgeno2haplo/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfcommonsamples/vcfcommonsamples/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfselectsamples/vcfselectsamples/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfleftalign/vcfleftalign/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcf2tsv/vcf2tsv/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfaddinfo/vcfaddinfo/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfannotate/vcfannotate/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfannotategenotypes/vcfannotategenotypes/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfcheck/vcfcheck/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfsort/vcfsort/0.0.1" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfgenotypes/vcfgenotypes/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfhethom/vcfhethom/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfbedintersect/vcfbedintersect/0.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/anton/vcfdistance/vcfdistance/0.0.2" />
</section>
<section id="peak_calling" name="NGS: Peak Calling" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.5.0" />
Expand Down Expand Up @@ -1059,6 +1045,7 @@
<tool id="Count1" />
</section>
<section id="plots" name="Graph/Display Data" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/devteam/xy_plot/XY_Plot_1/1.0.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/circos/circgraph/0.9-RC2" />
<tool id="toolshed.g2.bx.psu.edu/repos/peterjc/venn_list/venn_list/0.0.9" />
<tool id="toolshed.g2.bx.psu.edu/repos/guerler/charts/charts/1.0.0" />
Expand Down Expand Up @@ -1561,6 +1548,7 @@
</section>
<section id="ncbi_sra_tools" name="NCBI SRA Tools" version="">
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.8.1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.8.1.2" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.3" />
<tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.8.1.2" />
Expand Down
Loading

0 comments on commit 34a4dd4

Please sign in to comment.