| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | AB | |
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1 | Tool Shed URL | Repository | Owner | Revision | Panel Section | Repo Dep | Tool Dep | Tool | Id | Version | Tool + Version | Using | Command | |||||||||||||||
2 | https://testtoolshed.g2.bx.psu.edu/ | download_ref | pitagora | 8e177a318c8c | Pitagora Tools | No | No | Download References | download_ref | 0.0.1 | download_ref 0.0.1 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n download_ref -o pitagora -r 8e177a318c8c --panel-section-name "Pitagora Tools" --repository-deps --tool-deps | |||||||||||||||
3 | https://testtoolshed.g2.bx.psu.edu/ | filebrowser | pitagora | d2eb5a5a26a3 | Pitagora Tools | No | No | Local File | filebrowser | 1.0.0 | filebrowser 1.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n filebrowser -o pitagora -r d2eb5a5a26a3 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps | |||||||||||||||
4 | https://testtoolshed.g2.bx.psu.edu/ | imp_exp | pitagora | 4c225e57d44b | Pitagora Tools | No | No | Export | export | 1.0.0 | export 1.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n imp_exp -o pitagora -r 4c225e57d44b --panel-section-name "Pitagora Tools" --repository-deps --tool-deps | |||||||||||||||
5 | https://testtoolshed.g2.bx.psu.edu/ | imp_exp | pitagora | 4c225e57d44b | Pitagora Tools | No | No | Import | import | 1.0.0 | import 1.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n imp_exp -o pitagora -r 4c225e57d44b --panel-section-name "Pitagora Tools" --repository-deps --tool-deps | |||||||||||||||
6 | https://testtoolshed.g2.bx.psu.edu/ | sailfish_linux | pitagora | 655e814b3dc3 | RNA-seq | Yes | Yes | Sailfish | sailfish | 0.6.3 | sailfish 0.6.3 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n sailfish_linux -o pitagora -r 655e814b3dc3 --panel-section-name "RNA-seq" --repository-deps --tool-deps | |||||||||||||||
7 | https://testtoolshed.g2.bx.psu.edu/ | sratoolkit_centos | pitagora | b88e52ddb532 | NGS Tools | Yes | Yes | Extract reads | fastq_dump | 2.4.5 | fastq_dump 2.4.5 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n sratoolkit_centos -o pitagora -r b88e52ddb532 --panel-section-name "NGS Tools" --repository-deps --tool-deps | |||||||||||||||
8 | https://testtoolshed.g2.bx.psu.edu/ | unix_tools | pitagora | 8fd5091a4091 | Pitagora Tools | No | No | sed | sed | 1.0.0 | sed 1.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n unix_tools -o pitagora -r 8fd5091a4091 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps | |||||||||||||||
9 | https://testtoolshed.g2.bx.psu.edu/ | unix_tools | pitagora | 8fd5091a4091 | Pitagora Tools | No | No | awk | awk | 0.0.1 | awk 0.0.1 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://testtoolshed.g2.bx.psu.edu/ -n unix_tools -o pitagora -r 8fd5091a4091 --panel-section-name "Pitagora Tools" --repository-deps --tool-deps | |||||||||||||||
10 | https://toolshed.g2.bx.psu.edu/ | bam_to_sam | devteam | 250151b4d934 | NGS Tools | Yes | Yes | BAM-to-SAM | bam_to_sam | 1.0.4 | bam_to_sam 1.0.4 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bam_to_sam -o devteam -r 250151b4d934 --panel-section-name "NGS Tools" --repository-deps --tool-deps | |||||||||||||||
11 | https://toolshed.g2.bx.psu.edu/ | bedtools | iuc | 82aac94b06c3 | BED Tools | Yes | Yes | Intersect interval files | bedtools_intersectbed | 2.22.0 | bedtools_intersectbed 2.22.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bedtools -o iuc -r 82aac94b06c3 --panel-section-name "BED Tools" --repository-deps --tool-deps | |||||||||||||||
12 | https://toolshed.g2.bx.psu.edu/ | bowtie2 | devteam | ceb6467e276c | NGS Tools | Yes | Yes | Bowtie2 | bowtie2 | 0.4 | bowtie2 0.4 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bowtie2 -o devteam -r ceb6467e276c --panel-section-name "NGS Tools" --repository-deps --tool-deps | |||||||||||||||
13 | https://toolshed.g2.bx.psu.edu/ | bsfcall | yutaka-saito | f274c166e738 | BS-seq | No | Yes | bsfcall | bsfcall | 1.0.0 | bsfcall 1.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bsfcall -o yutaka-saito -r f274c166e738 --panel-section-name "BS-seq" --repository-deps --tool-deps | |||||||||||||||
14 | https://toolshed.g2.bx.psu.edu/ | bwa_wrappers | devteam | b4427dbb6ced | NGS Tools | Yes | Yes | Map with BWA for Illumina | bwa_wrapper | 1.0.2 | bwa_wrapper 1.0.2 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n bwa_wrappers -o devteam -r b4427dbb6ced --panel-section-name "NGS Tools" --repository-deps --tool-deps | |||||||||||||||
15 | https://toolshed.g2.bx.psu.edu/ | commet | yutaka-saito | dfdfbdd47b32 | BS-seq | No | Yes | ComMet | ComMet | 1.0.0 | ComMet 1.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n commet -o yutaka-saito -r dfdfbdd47b32 --panel-section-name "BS-seq" --repository-deps --tool-deps | |||||||||||||||
16 | https://toolshed.g2.bx.psu.edu/ | cuffdiff | devteam | 604fa75232a2 | RNA-seq | Yes | Yes | Cuffdiff | cuffdiff | 0.0.7 | cuffdiff 0.0.7 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n cuffdiff -o devteam -r 604fa75232a2 --panel-section-name "RNA-seq" --repository-deps --tool-deps | |||||||||||||||
17 | https://toolshed.g2.bx.psu.edu/ | cufflinks | devteam | 5346d5eea8b1 | RNA-seq | Yes | Yes | Cufflinks | cufflinks | 2.2.1.0 | cufflinks 2.2.1.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n cufflinks -o devteam -r 5346d5eea8b1 --panel-section-name "RNA-seq" --repository-deps --tool-deps | |||||||||||||||
18 | https://toolshed.g2.bx.psu.edu/ | cuffmerge | devteam | b6e3849293b1 | RNA-seq | Yes | Yes | Cuffmerge | cuffmerge | 2.2.1.0 | cuffmerge 2.2.1.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n cuffmerge -o devteam -r b6e3849293b1 --panel-section-name "RNA-seq" --repository-deps --tool-deps | |||||||||||||||
19 | https://toolshed.g2.bx.psu.edu/ | elapsed_time | pitagora | 6ea5fd3cbf6a | Pitagora Tools | Yes | Yes | Elapsed time | elapsed_time | 1.0 | elapsed_time 1.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n elapsed_time -o pitagora -r 6ea5fd3cbf6a --panel-section-name "Pitagora Tools" --repository-deps --tool-deps | |||||||||||||||
20 | https://toolshed.g2.bx.psu.edu/ | fastqc | devteam | 0b201de108b9 | NGS Tools | Yes | Yes | FastQC | fastqc | 0.63 | fastqc 0.63 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n fastqc -o devteam -r 0b201de108b9 --panel-section-name "NGS Tools" --repository-deps --tool-deps | |||||||||||||||
21 | https://toolshed.g2.bx.psu.edu/ | fastq_mcf | jjohnson | b61f1466ce8f | NGS Tools | Yes | Yes | FastqMcf | fastq_mcf | 1.0 | fastq_mcf 1.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n fastq_mcf -o jjohnson -r b61f1466ce8f --panel-section-name "NGS Tools" --repository-deps --tool-deps | |||||||||||||||
22 | https://toolshed.g2.bx.psu.edu/ | join | devteam | de21bdbb8d28 | General | Yes | Yes | Join | join | 1.0.0 | join 1.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n join -o devteam -r de21bdbb8d28 --panel-section-name "General" --repository-deps --tool-deps | |||||||||||||||
23 | https://toolshed.g2.bx.psu.edu/ | macs | devteam | ae2ec275332a | ChIP-seq | Yes | Yes | MACS | macs | 1.0.1 | macs 1.0.1 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n macs -o devteam -r ae2ec275332a --panel-section-name "ChIP-seq" --repository-deps --tool-deps | |||||||||||||||
24 | https://toolshed.g2.bx.psu.edu/ | macs14 | ryo-tas | c23082638ba0 | ChIP-seq | Yes | Yes | MACS14 | macs14 | 1.4.2 | macs14 1.4.2 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n macs14 -o ryo-tas -r c23082638ba0 --panel-section-name "ChIP-seq" --repository-deps --tool-deps | |||||||||||||||
25 | https://toolshed.g2.bx.psu.edu/ | macs2 | iuc | 859c982b1f7f | ChIP-seq | Yes | Yes | MACS2 callpeak | macs2_callpeak | 2.1.0.20140616.0 | macs2_callpeak 2.1.0.20140616.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n macs2 -o iuc -r 859c982b1f7f --panel-section-name "ChIP-seq" --repository-deps --tool-deps | |||||||||||||||
26 | https://toolshed.g2.bx.psu.edu/ | picard | devteam | 379fdf4c41ac | Picard | Yes | Yes | MarkDuplicates | picard_MarkDuplicates | 1.126.0 | picard_MarkDuplicates 1.126.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n picard -o devteam -r 379fdf4c41ac --panel-section-name "Picard" --repository-deps --tool-deps | |||||||||||||||
27 | https://toolshed.g2.bx.psu.edu/ | sam2interval | devteam | 8c737b8ddc45 | NGS Tools | No | No | Convert SAM | sam2interval | 1.0.1 | sam2interval 1.0.1 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sam2interval -o devteam -r 8c737b8ddc45 --panel-section-name "NGS Tools" --repository-deps --tool-deps | |||||||||||||||
28 | https://toolshed.g2.bx.psu.edu/ | sam_to_bam | devteam | 8176b2575aa1 | NGS Tools | Yes | Yes | SAM-to-BAM | sam_to_bam | 1.1.4 | sam_to_bam 1.1.4 | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sam_to_bam -o devteam -r 8176b2575aa1 --panel-section-name "NGS Tools" --repository-deps --tool-deps | ||||||||||||||||
29 | https://toolshed.g2.bx.psu.edu/ | sicer | devteam | 82a8234e03f2 | ChIP-seq | Yes | Yes | SICER | peakcalling_sicer | 0.0.1 | peakcalling_sicer 0.0.1 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sicer -o devteam -r 82a8234e03f2 --panel-section-name "ChIP-seq" --repository-deps --tool-deps | |||||||||||||||
30 | https://toolshed.g2.bx.psu.edu/ | snpsift | iuc | 9e8280e19338 | SnpSift | Yes | Yes | SnpSift Annotate | snpSift_annotate | 4.0.0 | snpSift_annotate 4.0.0 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n snpsift -o iuc -r 9e8280e19338 --panel-section-name "SnpSift" --repository-deps --tool-deps | |||||||||||||||
31 | https://toolshed.g2.bx.psu.edu/ | sql_tools | sem4j | 51847f1c0acb | SQL Tools | No | No | SQL | sqlite | 0.4 | sqlite 0.4 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n sql_tools -o sem4j -r 51847f1c0acb --panel-section-name "SQL Tools" --repository-deps --tool-deps | |||||||||||||||
32 | https://toolshed.g2.bx.psu.edu/ | tophat2 | devteam | 81f97e12e573 | RNA-seq | Yes | Yes | Tophat2 | tophat2 | 0.7 | tophat2 0.7 | using | python ~/galaxy-dist/scripts/api/install_tool_shed_repositories.py -a 126a89c98a5d1a2c234edf2651024a03 -l http://localhost:8080 -u https://toolshed.g2.bx.psu.edu/ -n tophat2 -o devteam -r 81f97e12e573 --panel-section-name "RNA-seq" --repository-deps --tool-deps | |||||||||||||||
33 | (pre-installed) | - | - | - | - | - | - | Join two Datasets | gops_join_1 | 2.0.2 | gops_join_1 2.0.2 | using | ||||||||||||||||
34 | (pre-installed) | - | - | - | - | - | - | Count | count | 1.0.0 | count 1.0.0 | using | ||||||||||||||||
35 | (pre-installed) | - | - | - | - | - | - | Cut | cut | 1.0.2 | cut 1.0.2 | using | ||||||||||||||||
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