Mercurial > repos > iuc > package_samtools_1_2
annotate tool_dependencies.xml @ 1:f6ae3ba3f3c1 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
| author | iuc |
|---|---|
| date | Fri, 17 Jul 2015 11:11:30 -0400 |
| parents | 6eea04363026 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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3 <package name="ncurses" version="5.9"> |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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4 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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changeset
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5 </package> |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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changeset
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6 <package name="zlib" version="1.2.8"> |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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0
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changeset
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7 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
0
diff
changeset
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8 </package> |
| 0 | 9 <package name="samtools" version="1.2"> |
| 10 <install version="1.0"> | |
| 11 <actions_group> | |
| 12 <actions architecture="x86_64" os="linux"> | |
| 13 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action> | |
| 14 <action type="move_directory_files"> | |
| 15 <source_directory>.</source_directory> | |
| 16 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 17 </action> | |
| 18 </actions> | |
| 19 <actions> | |
| 20 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action> | |
| 21 <action type="set_environment_for_install"> | |
| 22 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
| 23 <package name="ncurses" version="5.9" /> | |
| 24 </repository> | |
| 25 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
| 26 <package name="zlib" version="1.2.8" /> | |
| 27 </repository> | |
| 28 </action> | |
| 29 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action> | |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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0
diff
changeset
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30 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action> |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
0
diff
changeset
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31 <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> |
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f6ae3ba3f3c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
0
diff
changeset
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32 <action type="make_install" /> |
| 0 | 33 <action type="move_file"> |
| 34 <source>samtools</source> | |
| 35 <destination>$INSTALL_DIR/bin</destination> | |
| 36 </action> | |
| 37 </actions> | |
| 38 <action type="set_environment"> | |
| 39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 40 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 41 </action> | |
| 42 </actions_group> | |
| 43 </install> | |
| 44 <readme> | |
| 45 Program: samtools (Tools for alignments in the SAM format) | |
| 46 Version: 1.2 | |
| 47 | |
| 48 Usage: samtools <command> [options] | |
| 49 | |
| 50 Commands: | |
| 51 -- indexing | |
| 52 faidx index/extract FASTA | |
| 53 index index alignment | |
| 54 -- editing | |
| 55 calmd recalculate MD/NM tags and '=' bases | |
| 56 fixmate fix mate information | |
| 57 reheader replace BAM header | |
| 58 rmdup remove PCR duplicates | |
| 59 targetcut cut fosmid regions (for fosmid pool only) | |
| 60 -- file operations | |
| 61 bamshuf shuffle and group alignments by name | |
| 62 cat concatenate BAMs | |
| 63 merge merge sorted alignments | |
| 64 mpileup multi-way pileup | |
| 65 sort sort alignment file | |
| 66 split splits a file by read group | |
| 67 bam2fq converts a BAM to a FASTQ | |
| 68 -- stats | |
| 69 bedcov read depth per BED region | |
| 70 depth compute the depth | |
| 71 flagstat simple stats | |
| 72 idxstats BAM index stats | |
| 73 phase phase heterozygotes | |
| 74 stats generate stats (former bamcheck) | |
| 75 -- viewing | |
| 76 flags explain BAM flags | |
| 77 tview text alignment viewer | |
| 78 view SAM<->BAM<->CRAM conversion | |
| 79 </readme> | |
| 80 </package> | |
| 81 </tool_dependency> |