Mercurial > repos > iuc > package_samtools_0_1_19
annotate tool_dependencies.xml @ 7:8b98841b6b2f draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 18 Feb 2015 11:32:40 -0500 |
| parents | 632f1a03db92 |
| children | 0e56e4dac6e7 |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 2 | 3 <package name="ncurses" version="5.9"> |
| 7 | 4 <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 6 | 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" /> | |
| 2 | 8 </package> |
| 0 | 9 <package name="samtools" version="0.1.19"> |
| 10 <install version="1.0"> | |
| 11 <actions> | |
| 12 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action> | |
| 2 | 13 <action type="set_environment_for_install"> |
| 7 | 14 <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 2 | 15 <package name="ncurses" version="5.9" /> |
| 16 </repository> | |
| 6 | 17 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 18 <package name="zlib" version="1.2.8" /> | |
| 19 </repository> | |
| 2 | 20 </action> |
| 7 | 21 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action> |
| 5 | 22 <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$NCURSES_LIB_PATH|g" Makefile</action> |
| 0 | 23 <action type="shell_command">make</action> |
| 24 <action type="move_file"> | |
| 25 <source>samtools</source> | |
| 26 <destination>$INSTALL_DIR/bin</destination> | |
| 27 </action> | |
| 28 <action type="set_environment"> | |
| 2 | 29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
| 0 | 30 </action> |
| 31 </actions> | |
| 32 </install> | |
| 33 <readme> | |
| 34 Program: samtools (Tools for alignments in the SAM format) | |
| 2 | 35 Version: 0.1.19 |
| 0 | 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 | |
|
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54195f1d4b0f
Also install bcftools and misc utility commands when installing samtools.
Jim Johnson <jj@umn.edu>
parents:
0
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changeset
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56 |
| 2 | 57 Requirements: libncurses header files |
| 0 | 58 </readme> |
| 59 </package> | |
| 60 </tool_dependency> |