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samtools-software
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samtools-software [2017/02/05 11:38] joguya |
samtools-software [2021/01/17 10:22] (current) 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: 1.11 |
| - | * Updated: February, 2017 | + | |
| * Added: February, 2015 | * Added: February, 2015 | ||
| - | * Link: http:// | + | |
| + | | ||
| ===== Usage ===== | ===== Usage ===== | ||
| Line 12: | Line 12: | ||
| < | < | ||
| - | 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: | ||
| - | < | + | < |
| - | $ cd /tmp | + | $ wget https:// |
| - | $ wget -qO- "https:// | + | $ tar xf samtools-1.11.tar.bz2 |
| - | $ cd samtools-1.3.1/ | + | $ cd samtools-1.11 |
| - | $ 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/ | ||
samtools-software.1486294723.txt.gz · Last modified: 2017/02/05 11:38 by joguya
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