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cluster:73 [2020/04/06 17:03] hmeij07 [Amber] |
cluster:73 [2020/06/18 19:03] hmeij07 [Sequencing Tools] |
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on either cottontail2 or node n33 located at / | on either cottontail2 or node n33 located at / | ||
Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
+ | |||
+ | ====== Sequencing Tools ====== | ||
+ | |||
+ | * macs python package (macs2 see below) | ||
+ | * http:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH="/ | ||
+ | export LD_LIBRARY_PATH="/ | ||
+ | Successfully installed macs-1.4.3 | ||
+ | |||
+ | # or change python version to | ||
+ | # ls / | ||
+ | / | ||
+ | |||
+ | |||
+ | export PATH="/ | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | which gcc: / | ||
+ | which python: / | ||
+ | which perl: / | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | which R: / | ||
+ | ldd / | ||
+ | |||
+ | java --version: java 12.0.2 2019-07-16 # / | ||
+ | java -jar / | ||
+ | USAGE: PicardCommandLine <program name> [-h] | ||
+ | |||
+ | export PATH=/ | ||
+ | bedtools --version: bedtools v2.29.2 | ||
+ | |||
+ | </ | ||
====== Deep Learning Software Stack ====== | ====== Deep Learning Software Stack ====== | ||
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====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** CPU ONLY ** | ||
+ | |||
+ | * / | ||
+ | * lmp_mpi, lmp_serial | ||
+ | * consult this file for packages installed and compilations | ||
+ | * / | ||
+ | * should work on all queues | ||
+ | * sample script in ~hmeij/ | ||
+ | |||
+ | |||
+ | ** CPU or GPU ** | ||
* / | * / | ||
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* program: Matlab, link to binary is ' | * program: Matlab, link to binary is ' | ||
- | * R2018a, campus wide license so no more restrictions on licenses | + | * R2020a, campus wide license so no more restrictions on licenses |
- | * No Distributed Computing Engine (for now) | + | * No Distributed Computing Engine |
- | * install dir: / | + | * install dir: / |
* docs & www: http:// | * docs & www: http:// | ||
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* http:// | * http:// | ||
- | Details about the Matlab configuration/ | + | |
====== Stata ====== | ====== Stata ====== |