samtools-software
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samtools-software [2017/02/05 11:38] – joguya | samtools-software [2019/09/03 22:00] – 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. | ||
- | * Latest Version: 1.3.1 | + | * Latest Version: 1.9 |
- | * Updated: February, 2017 | + | |
* Added: February, 2015 | * Added: February, 2015 | ||
- | * Link: http:// | + | |
+ | | ||
===== Usage ===== | ===== Usage ===== | ||
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Load a particular version of samtools: | Load a particular version of samtools: | ||
- | < | + | < |
===== Installation ===== | ===== Installation ===== | ||
Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ cd /tmp | + | $ wget https:// |
- | $ wget -qO- "https:// | + | $ tar xf samtools-1.9.tar.bz2 |
- | $ cd samtools-1.3.1/ | + | $ cd samtools-1.9 |
- | $ scl enable devtoolset-2 bash | + | # install a newer compiler from Red Hat software collections |
- | $ sudo mkdir / | + | $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ |
- | $ sudo chown -R joguya: | + | $ scl enable devtoolset-7 bash |
- | $ ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/ | + | $ ./configure --enable-plugins --enable-libcurl --prefix=/ |
- | $ make all install-htslib | + | $ make |
- | $ make install install-htslib | + | $ sudo mkdir -p / |
- | $ sudo chown -R root:root / | + | $ sudo chown aorth / |
- | </ | + | $ make install |
+ | $ sudo chown -R root:root / | ||
+ | |||
+ | This links against htslib installed as a module in htslib/1.9. |
samtools-software.txt · Last modified: 2022/06/23 09:35 by aorth