samtools-software
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samtools-software [2015/02/12 11:22] – created joguya | samtools-software [2021/01/17 10:22] – 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.txt · Last modified: 2022/06/23 09:35 by aorth