samtools-software
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samtools-software [2015/06/09 16:40] – aorth | samtools-software [2021/09/05 10:32] – aorth | ||
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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. | ||
- | * Version: 1.2 | + | * Latest |
* Added: February, 2015 | * Added: February, 2015 | ||
- | * Link: http://samtools.sourceforge.net/ | + | |
+ | | ||
- | === Usage === | + | ===== Usage ===== |
Show all available versions of samtools: | Show all available versions of samtools: | ||
< | < | ||
- | Load a particular version of samtools: | + | Load a particular version of samtools |
- | < | + | < |
+ | $ samtools</ | ||
- | === Installation === | + | ===== Installation |
Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ git clone git@github.com:samtools/ | + | $ wget https://github.com/samtools/ |
- | $ cd samtools | + | $ tar xf samtools-1.13.tar.bz2 |
- | $ git checkout | + | $ cd samtools-1.13 |
- | $ sudo mkdir -p / | + | # install a newer compiler from Red Hat software collections |
- | $ sudo chown joguya: | + | $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ |
+ | $ scl enable devtoolset-7 bash | ||
+ | $ ./configure --enable-plugins --enable-libcurl --prefix=/ | ||
$ make | $ make | ||
- | $ make prefix=/ | + | $ sudo mkdir -p / |
- | $ sudo chown -R root:root / | + | $ sudo chown aorth /export/ |
+ | $ make install | ||
+ | $ sudo chown -R root:root / | ||
+ | |||
+ | This links against htslib/ |
samtools-software.txt · Last modified: 2022/06/23 09:35 by aorth