Mercurial > repos > iuc > package_samtools_1_2
annotate tool_dependencies.xml @ 8:9cd278d52bb6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 6dbfa1702715b9829933c743ec0a6ace61303a74
| author | iuc |
|---|---|
| date | Tue, 07 Jul 2015 06:21:42 -0400 |
| parents | 8d3a21e43004 |
| children | 192f00129358 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="ncurses" version="5.9"> | |
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77e0e0891773
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 48fbe322d0f3ec023186989104ae4f4188b03a1d
iuc
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changeset
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4 <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
| 6 <package name="zlib" version="1.2.8"> | |
| 7 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 9 <package name="samtools" version="1.2"> | |
| 10 <install version="1.0"> | |
| 11 <actions_group> | |
| 12 <actions> | |
| 13 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> | |
| 14 <action type="set_environment_for_install"> | |
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4
77e0e0891773
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 48fbe322d0f3ec023186989104ae4f4188b03a1d
iuc
parents:
3
diff
changeset
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15 <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 16 <package name="ncurses" version="5.9" /> |
| 17 </repository> | |
| 18 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 19 <package name="zlib" version="1.2.8" /> | |
| 20 </repository> | |
| 21 </action> | |
| 22 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> | |
| 23 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action> | |
| 24 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> | |
| 25 <action type="shell_command">make</action> | |
| 26 <action type="move_file"> | |
| 27 <source>samtools</source> | |
| 28 <destination>$INSTALL_DIR/bin</destination> | |
| 29 </action> | |
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8d3a21e43004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
iuc
parents:
6
diff
changeset
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30 <action type="shell_command">cd htslib-1.2.1 && make bgzip tabix</action> |
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8d3a21e43004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
iuc
parents:
6
diff
changeset
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31 <action type="move_file"> |
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8
9cd278d52bb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 6dbfa1702715b9829933c743ec0a6ace61303a74
iuc
parents:
7
diff
changeset
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32 <source>htslib-1.2.1/bgzip</source> |
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7
8d3a21e43004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
iuc
parents:
6
diff
changeset
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33 <destination>$INSTALL_DIR/bin</destination> |
|
8d3a21e43004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
iuc
parents:
6
diff
changeset
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34 </action> |
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8d3a21e43004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
iuc
parents:
6
diff
changeset
|
35 <action type="move_file"> |
|
8
9cd278d52bb6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 6dbfa1702715b9829933c743ec0a6ace61303a74
iuc
parents:
7
diff
changeset
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36 <source>htslib-1.2.1/tabix</source> |
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7
8d3a21e43004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
iuc
parents:
6
diff
changeset
|
37 <destination>$INSTALL_DIR/bin</destination> |
|
8d3a21e43004
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit 0347bb0b05cae8686a0c2a51285a80f0dffc3b54
iuc
parents:
6
diff
changeset
|
38 </action> |
| 0 | 39 </actions> |
| 40 <action type="set_environment"> | |
| 41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 42 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 43 </action> | |
| 44 </actions_group> | |
| 45 </install> | |
| 46 <readme> | |
| 47 Program: samtools (Tools for alignments in the SAM format) | |
| 48 Version: 1.2 | |
| 49 | |
| 50 Usage: samtools <command> [options] | |
| 51 | |
| 52 Commands: | |
| 53 -- indexing | |
| 54 faidx index/extract FASTA | |
| 55 index index alignment | |
| 56 -- editing | |
| 57 calmd recalculate MD/NM tags and '=' bases | |
| 58 fixmate fix mate information | |
| 59 reheader replace BAM header | |
| 60 rmdup remove PCR duplicates | |
| 61 targetcut cut fosmid regions (for fosmid pool only) | |
| 62 -- file operations | |
| 63 bamshuf shuffle and group alignments by name | |
| 64 cat concatenate BAMs | |
| 65 merge merge sorted alignments | |
| 66 mpileup multi-way pileup | |
| 67 sort sort alignment file | |
| 68 split splits a file by read group | |
| 69 bam2fq converts a BAM to a FASTQ | |
| 70 -- stats | |
| 71 bedcov read depth per BED region | |
| 72 depth compute the depth | |
| 73 flagstat simple stats | |
| 74 idxstats BAM index stats | |
| 75 phase phase heterozygotes | |
| 76 stats generate stats (former bamcheck) | |
| 77 -- viewing | |
| 78 flags explain BAM flags | |
| 79 tview text alignment viewer | |
| 80 view SAM<->BAM<->CRAM conversion | |
| 81 </readme> | |
| 82 </package> | |
| 83 </tool_dependency> |