Mercurial > repos > iuc > package_samtools_1_1
annotate tool_dependencies.xml @ 8:50e5ac891216 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_1 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
| author | iuc |
|---|---|
| date | Tue, 22 Dec 2015 19:38:38 -0500 |
| parents | f9a023ce60e3 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 2 | 3 <package name="ncurses" version="5.9"> |
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50e5ac891216
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_1 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
parents:
7
diff
changeset
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4 <repository changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 2 | 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> | |
| 0 | 9 <package name="samtools" version="1.1"> |
| 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-1.1-Linux-x86_64.tgz</action> | |
| 14 <action type="move_directory_files"> | |
| 15 <source_directory>.</source_directory> | |
| 16 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 17 </action> | |
| 18 </actions> | |
| 19 <actions> | |
| 20 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2</action> | |
| 21 <action type="set_environment_for_install"> | |
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8
50e5ac891216
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_1 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
parents:
7
diff
changeset
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22 <repository changeset_revision="d14cd2be7d8d" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 23 <package name="ncurses" version="5.9" /> |
| 24 </repository> | |
| 25 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 26 <package name="zlib" version="1.2.8" /> | |
| 27 </repository> | |
| 28 </action> | |
|
7
f9a023ce60e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_1 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
6
diff
changeset
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29 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action> |
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f9a023ce60e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_1 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
parents:
6
diff
changeset
|
30 <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action> |
| 0 | 31 <action type="shell_command">make</action> |
| 32 <action type="move_file"> | |
| 33 <source>samtools</source> | |
| 34 <destination>$INSTALL_DIR/bin</destination> | |
| 35 </action> | |
| 36 </actions> | |
| 37 <action type="set_environment"> | |
| 38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 39 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> | |
| 40 </action> | |
| 41 </actions_group> | |
| 42 </install> | |
| 43 <readme> | |
| 44 Program: samtools (Tools for alignments in the SAM format) | |
| 45 Version: 1.1 (using htslib 1.1) | |
| 46 | |
| 47 Usage: samtools <command> [options] | |
| 48 | |
| 49 Commands: | |
| 50 -- indexing | |
| 51 faidx index/extract FASTA | |
| 52 index index alignment | |
| 53 -- editing | |
| 54 calmd recalculate MD/NM tags and '=' bases | |
| 55 fixmate fix mate information | |
| 56 reheader replace BAM header | |
| 57 rmdup remove PCR duplicates | |
| 58 targetcut cut fosmid regions (for fosmid pool only) | |
| 59 -- file operations | |
| 60 bamshuf shuffle and group alignments by name | |
| 61 cat concatenate BAMs | |
| 62 merge merge sorted alignments | |
| 63 mpileup multi-way pileup | |
| 64 sort sort alignment file | |
| 65 split splits a file by read group | |
| 66 bam2fq converts a BAM to a FASTQ | |
| 67 -- stats | |
| 68 bedcov read depth per BED region | |
| 69 depth compute the depth | |
| 70 flagstat simple stats | |
| 71 idxstats BAM index stats | |
| 72 phase phase heterozygotes | |
| 73 stats generate stats (former bamcheck) | |
| 74 -- viewing | |
| 75 flags explain BAM flags | |
| 76 tview text alignment viewer | |
| 77 view SAM<->BAM<->CRAM conversion | |
| 78 </readme> | |
| 79 </package> | |
| 80 </tool_dependency> |