Mercurial > repos > jjohnson > package_samtools_0_1_19
comparison tool_dependencies.xml @ 0:06697b4877f9 draft default tip
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| author | jjohnson |
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| date | Tue, 03 Sep 2013 11:48:30 -0400 |
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| -1:000000000000 | 0:06697b4877f9 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="samtools" version="0.1.19"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> | |
| 7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | |
| 8 <action type="shell_command">make</action> | |
| 9 <action type="shell_command">chmod ugo+rx misc/*.p?</action> | |
| 10 <action type="shell_command">mkdir misc/bin</action> | |
| 11 <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action> | |
| 12 <action type="move_file"> | |
| 13 <source>samtools</source> | |
| 14 <destination>$INSTALL_DIR/bin</destination> | |
| 15 </action> | |
| 16 <action type="move_file"> | |
| 17 <source>bcftools/bcftools</source> | |
| 18 <destination>$INSTALL_DIR/bin</destination> | |
| 19 </action> | |
| 20 <action type="move_file"> | |
| 21 <source>bcftools/vcfutils.pl</source> | |
| 22 <destination>$INSTALL_DIR/bin</destination> | |
| 23 </action> | |
| 24 <action type="move_directory_files"> | |
| 25 <source_directory>misc/bin</source_directory> | |
| 26 <destination_directory>$INSTALL_DIR/bin</destination_directory> | |
| 27 </action> | |
| 28 <action type="set_environment"> | |
| 29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 30 </action> | |
| 31 </actions> | |
| 32 </install> | |
| 33 <readme> | |
| 34 Program: samtools (Tools for alignments in the SAM format) | |
| 35 Version: 0.1.19 | |
| 36 | |
| 37 Usage: samtools <command> [options] | |
| 38 | |
| 39 Command: view SAM<->BAM conversion | |
| 40 sort sort alignment file | |
| 41 mpileup multi-way pileup | |
| 42 depth compute the depth | |
| 43 faidx index/extract FASTA | |
| 44 tview text alignment viewer | |
| 45 index index alignment | |
| 46 idxstats BAM index stats (r595 or later) | |
| 47 fixmate fix mate information | |
| 48 flagstat simple stats | |
| 49 calmd recalculate MD/NM tags and '=' bases | |
| 50 merge merge sorted alignments | |
| 51 rmdup remove PCR duplicates | |
| 52 reheader replace BAM header | |
| 53 cat concatenate BAMs | |
| 54 targetcut cut fosmid regions (for fosmid pool only) | |
| 55 phase phase heterozygotes | |
| 56 | |
| 57 This also installs bcftools and misc utility commands: | |
| 58 bcftools | |
| 59 vcfutils.pl | |
| 60 ace2sam | |
| 61 bamcheck | |
| 62 blast2sam.pl | |
| 63 bowtie2sam.pl | |
| 64 export2sam.pl | |
| 65 interpolate_sam.pl | |
| 66 maq2sam-long | |
| 67 maq2sam-short | |
| 68 md5fa | |
| 69 md5sum-lite | |
| 70 novo2sam.pl | |
| 71 psl2sam.pl | |
| 72 sam2vcf.pl | |
| 73 samtools.pl | |
| 74 soap2sam.pl | |
| 75 varfilter.py | |
| 76 wgsim | |
| 77 wgsim_eval.pl | |
| 78 zoom2sam.pl | |
| 79 </readme> | |
| 80 </package> | |
| 81 </tool_dependency> |