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samtools-software
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samtools-software [2015/02/12 11:22] joguya created |
samtools-software [2021/01/17 10:22] (current) aorth |
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| ====== samtools ====== | ====== samtools ====== | ||
| - | * samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. | + | samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
| - | ==== v1.2 ==== | + | |
| - | | + | |
| * Added: February, 2015 | * Added: February, 2015 | ||
| - | * Link: http://samtools.sourceforge.net/ | + | |
| + | | ||
| - | === Usage === | + | ===== Usage ===== |
| - | | + | Show all available versions of samtools: |
| - | * Load samtools module: < | + | |
| - | === Installation === | + | < |
| - | * clone samtools repo & compile it< | + | |
| - | git clone git@github.com: | + | |
| - | cd samtools | + | |
| - | git checkout 1.2 | + | |
| - | sudo mkdir -p / | + | |
| - | sudo chown joguya: | + | |
| - | make | + | |
| - | make prefix=/ | + | |
| - | sudo chown -R root:root / | + | |
| - | * samtools module file< | + | |
| - | ##################################################################### | + | |
| - | ## | + | |
| - | ## samtools Modulefile | + | |
| - | ## by James Oguya < | + | |
| - | ## February, 2015 | + | |
| - | ## | + | |
| - | set appname | + | Load a particular |
| - | set version | + | |
| - | set prefix | + | |
| - | set exec_prefix | + | |
| - | set datarootdir | + | |
| - | set url " | + | |
| - | set msg "This module adds samtools v$version to various paths\n\nsamtools Official Site: $url\n" | + | |
| - | proc ModulesHelp { } { | + | < |
| - | puts stderr "$msg" | + | $ samtools</ |
| - | } | + | |
| - | module-whatis | + | ===== Installation ===== |
| + | Notes from the sysadmin during installation: | ||
| - | conflict | + | < |
| - | + | $ wget https:// | |
| - | prepend-path | + | $ tar xf samtools-1.11.tar.bz2 |
| - | prepend-path MANPATH | + | $ cd samtools-1.11 |
| - | </ | + | # install a newer compiler from Red Hat software collections |
| - | + | $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ | |
| - | * deploy the new module using ansible< | + | $ scl enable devtoolset-7 bash |
| + | $ ./ | ||
| + | $ make | ||
| + | $ sudo mkdir -p / | ||
| + | $ sudo chown aorth / | ||
| + | $ make install | ||
| + | $ sudo chown -R root:root / | ||
| + | This links against htslib/ | ||
samtools-software.1423740141.txt.gz · Last modified: 2015/02/12 11:22 by joguya
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