cluster:73
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cluster:73 [2020/01/14 14:57] hmeij07 [Paleogenomics Tools] |
cluster:73 [2020/02/18 13:46] hmeij07 [Python3] |
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| **[[cluster: | **[[cluster: | ||
| + | ===== Software ===== | ||
| The listings below will be updated as software is installed, location is / | The listings below will be updated as software is installed, location is / | ||
| Line 10: | Line 10: | ||
| Most of the compilations have been performed by Intel' | Most of the compilations have been performed by Intel' | ||
| - | The list of software was primarily compiled under RHEL5.1 but more recent compilation | + | Old compilations, |
| + | Newer compilations are done with CentOS 6.10 (since summer 2013) \\ | ||
| + | on either | ||
| + | Some compilations require 7.x and are in / | ||
| ====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
| Line 40: | Line 43: | ||
| </ | </ | ||
| + | |||
| + | * https:// | ||
| + | * BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. | ||
| + | |||
| + | < | ||
| + | |||
| + | # with local java jre1.8.0_212 | ||
| + | export PATH=/ | ||
| + | |||
| + | </ | ||
| + | |||
| ====== CD-HIT ====== | ====== CD-HIT ====== | ||
| Line 118: | Line 132: | ||
| ====== Python3 ====== | ====== Python3 ====== | ||
| + | |||
| + | Added to both versions\\ | ||
| + | pycuda\\ | ||
| + | --- // | ||
| + | |||
| + | Added to both 3.5.2 versions\\ | ||
| + | Successfully installed\\ | ||
| + | boto-2.49.0 boto3-1.12.0 botocore-1.15.0 gensim-3.8.1 jmespath-0.9.4 s3transfer-0.3.3 smart-open-1.9.0\\ | ||
| + | joblib, scikit-learn, | ||
| + | \\ | ||
| + | Requirement already satisfied: | ||
| + | keras keras-preprocessing keras-applications\\ | ||
| + | tensorflow (requires centos7)\\ | ||
| + | --- // | ||
| + | |||
| Added to both 3.5.2 versions\\ | Added to both 3.5.2 versions\\ | ||
| Line 2595: | Line 2624: | ||
| For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, | For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, | ||
| + | |||
| + | * program: GCC v 9.2.0 | ||
| + | * / | ||
| + | * note: libgomp disabled for nanopolish compile attempt | ||
| + | |||
| + | < | ||
| + | |||
| + | wget ftp:// | ||
| + | tar zxvf gcc-9.2.0.tar.gz | ||
| + | cd gcc-9.2.0 | ||
| + | ./ | ||
| + | ./configure --prefix=/ | ||
| + | make | ||
| + | make install | ||
| + | |||
| + | |||
| + | </ | ||
| * program: GCC v 4.8.4 | * program: GCC v 4.8.4 | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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