pear-software
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pear-software [2016/09/20 09:41] – created joguya | pear-software [2020/04/16 11:14] (current) – aorth | ||
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====== PEAR ====== | ====== PEAR ====== | ||
- | PEAR assembles Illumina paired-end reads if the DNA fragment sizes are smaller than twice the length | + | An ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes |
===== Information ===== | ===== Information ===== | ||
- | * Version: | + | * Version: |
* Added: September, 2016 | * Added: September, 2016 | ||
- | * Link: https://github.com/xflouris/PEAR | + | |
+ | | ||
===== Usage ===== | ===== Usage ===== | ||
Line 14: | Line 15: | ||
< | < | ||
- | Load pear | + | Load one version into your environment and run it: |
- | < | + | < |
+ | $ pear</ | ||
+ | |||
+ | Note: please use the '' | ||
===== Installation ====== | ===== Installation ====== | ||
Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
+ | |||
< | < | ||
$ cd /tmp | $ cd /tmp | ||
- | $ git clone https://github.com/ | + | $ wget https://depot.galaxyproject.org/software/pear/pear_0.9.6_src_all.tar.gz |
- | $ sudo mkdir -p /export/apps/pear/git-2c309dc | + | $ tar xf pear_0.9.6_src_all.tar.gz |
- | $ sudo chown -R joguya: | + | $ cd pear-0.9.6-src |
- | $ scl enable devtoolset-2 bash | + | $ scl enable devtoolset-7 bash |
- | $ ./ | + | $ ./configure --prefix=/ |
- | $ ./ | + | |
$ make | $ make | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo chown aorth / | ||
$ make install | $ make install | ||
- | $ sudo chown -R root:root / | + | $ sudo chown -R root:root / |
</ | </ | ||
+ | Note: I downloaded this from galaxyproject because the upstream site requires academic registration and I never received the confirmation mail to download the software. Also, this is the URL that is used by Conda. |
pear-software.1474364493.txt.gz · Last modified: 2016/09/20 09:41 by joguya