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samtools-software
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samtools-software [2017/06/30 14:40] aorth |
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 |
| * Added: February, 2015 | * Added: February, 2015 | ||
| - | * Updated: | + | * Updated: |
| * Link: http:// | * Link: http:// | ||
| Line 14: | Line 14: | ||
| 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 https:// | + | $ tar xf samtools-1.9.tar.bz2 |
| - | $ tar xf samtools-1.3.1.tar.bz2 | + | $ cd samtools-1.9 |
| - | $ cd samtools-1.3.1/ | + | # install a newer compiler from Red Hat software collections |
| - | $ scl enable devtoolset-2 bash | + | $ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++ |
| - | $ sudo mkdir / | + | $ scl enable devtoolset-7 bash |
| - | $ sudo chown -R joguya: | + | $ ./configure --enable-plugins --enable-libcurl --prefix=/ |
| - | $ ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/ | + | $ make |
| - | $ make all install-htslib | + | $ sudo mkdir -p / |
| - | $ make install install-htslib | + | $ sudo chown aorth / |
| - | $ sudo chown -R root:root / | + | $ make install |
| - | </ | + | $ sudo chown -R root:root / |
| + | |||
| + | This links against htslib installed as a module in htslib/1.9. | ||
samtools-software.txt · Last modified: 2021/01/17 10:22 by aorth
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