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annotate tool_dependencies.xml @ 2:b4f1eee85d8d draft default tip
planemo upload
| author | jmchilton |
|---|---|
| date | Sat, 04 Jul 2015 09:38:12 -0400 |
| parents | 58eb64dff5b4 |
| children |
| rev | line source |
|---|---|
| 2 | 1 <?xml version="1.0"?> |
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ebc6b1b18de6
planemo upload commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
diff
changeset
|
2 <tool_dependency> |
| 2 | 3 <package name="samtools" version="0.1.16"> |
| 4 <install version="1.0"> | |
| 5 <actions_group> | |
| 6 <actions os="linux" architecture="i386"> | |
| 7 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action> | |
| 8 <action type="move_directory_files"> | |
| 9 <source_directory>.</source_directory> | |
| 10 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 11 </action> | |
| 12 </actions> | |
| 13 <actions os="linux" architecture="x86_64"> | |
| 14 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action> | |
| 15 <action type="move_directory_files"> | |
| 16 <source_directory>.</source_directory> | |
| 17 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 18 </action> | |
| 19 </actions> | |
| 20 <actions os="darwin" architecture="i386"> | |
| 21 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action> | |
| 22 <action type="move_directory_files"> | |
| 23 <source_directory>.</source_directory> | |
| 24 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 25 </action> | |
| 26 </actions> | |
| 27 <actions os="darwin" architecture="x86_64"> | |
| 28 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action> | |
| 29 <action type="move_directory_files"> | |
| 30 <source_directory>.</source_directory> | |
| 31 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 32 </action> | |
| 33 </actions> | |
| 34 <actions> | |
| 35 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action> | |
| 36 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | |
| 37 <action type="shell_command">make</action> | |
| 38 <action type="move_file"> | |
| 39 <source>samtools</source> | |
| 40 <destination>$INSTALL_DIR/bin</destination> | |
| 41 </action> | |
| 42 <action type="move_file"> | |
| 43 <source>libbam.a</source> | |
| 44 <destination>$INSTALL_DIR/lib</destination> | |
| 45 </action> | |
| 46 </actions> | |
| 47 <action type="set_environment"> | |
| 48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 49 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> | |
| 50 </action> | |
| 51 </actions_group> | |
| 52 </install> | |
|
0
ebc6b1b18de6
planemo upload commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
diff
changeset
|
53 <readme> |
| 2 | 54 This is the last version of SAMTools to include the 'pileup' command. |
| 55 | |
| 56 Program: samtools (Tools for alignments in the SAM format) | |
| 57 Version: 0.1.16 (r963:234) | |
| 58 | |
| 59 Usage: samtools <command> [options] | |
| 60 | |
| 61 Command: view SAM<->BAM conversion | |
| 62 sort sort alignment file | |
| 63 pileup generate pileup output | |
| 64 mpileup multi-way pileup | |
| 65 depth compute the depth | |
| 66 faidx index/extract FASTA | |
| 67 tview text alignment viewer | |
| 68 index index alignment | |
| 69 idxstats BAM index stats (r595 or later) | |
| 70 fixmate fix mate information | |
| 71 glfview print GLFv3 file | |
| 72 flagstat simple stats | |
| 73 calmd recalculate MD/NM tags and '=' bases | |
| 74 merge merge sorted alignments | |
| 75 rmdup remove PCR duplicates | |
| 76 reheader replace BAM header | |
| 77 cat concatenate BAMs | |
| 78 targetcut cut fosmid regions (for fosmid pool only) | |
| 79 phase phase heterozygotes | |
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0
ebc6b1b18de6
planemo upload commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
diff
changeset
|
80 </readme> |
| 2 | 81 </package> |
|
0
ebc6b1b18de6
planemo upload commit 37c9a84ce3065ceab57cfb4cdd35a4a75d6ef223
peterjc
parents:
diff
changeset
|
82 </tool_dependency> |