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samtools-software
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samtools-software [2015/06/09 16:41] aorth |
samtools-software [2021/01/17 10:22] 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:// | + | |
| + | | ||
| ===== Usage ===== | ===== Usage ===== | ||
| Line 11: | 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: | ||
| - | < | + | < |
| - | $ git clone git@github.com:samtools/ | + | $ wget https://github.com/samtools/ |
| - | $ cd samtools | + | $ tar xf samtools-1.11.tar.bz2 |
| - | $ git checkout | + | $ cd samtools-1.11 |
| - | $ 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: 2021/01/17 10:22 by aorth
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