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cluster:73 [2020/03/30 18:30] hmeij07 [Amber] |
cluster:73 [2020/06/19 17:34] hmeij07 [Python3] |
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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 #2 ====== | ||
+ | |||
+ | * macs python package (macs2 see below) | ||
+ | * http:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | * https:// | ||
+ | * padillalab | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH="/ | ||
+ | export LD_LIBRARY_PATH="/ | ||
+ | Successfully installed macs-1.4.3 | ||
+ | |||
+ | # or change python version to | ||
+ | # ls / | ||
+ | / | ||
+ | |||
+ | # or change python version to | ||
+ | which python: / | ||
+ | pip list: Package | ||
+ | --------------- ------- | ||
+ | bowtie | ||
+ | MACS2 | ||
+ | numpy | ||
+ | picard | ||
+ | scipy 1.4.1 | ||
+ | |||
+ | |||
+ | 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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* portainer | * portainer | ||
* consult [[cluster: | * consult [[cluster: | ||
+ | * QAC | ||
====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
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* BCFtools: | * BCFtools: | ||
* HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
+ | * Archeology (kbrunson) | ||
< | < | ||
Line 79: | Line 136: | ||
* https:// | * https:// | ||
* recipe at / | * recipe at / | ||
+ | * Starrlab | ||
OpenStructure relies on these applications and Python 2.7.15 (see python2 section). | OpenStructure relies on these applications and Python 2.7.15 (see python2 section). | ||
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* add the bin/ directory to your PATH (see examples on this page) | * add the bin/ directory to your PATH (see examples on this page) | ||
* http:// | * http:// | ||
+ | * fcolanlab (wmei, ndelgaudio) | ||
====== Spyder ====== | ====== Spyder ====== | ||
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====== Python3 ====== | ====== Python3 ====== | ||
- | Added to both versions\\ | + | * Python 3.8.3 |
+ | * / | ||
+ | * most packages found on this page | ||
+ | * picked up mpirun from miniconda2 apps (that may be a problem) | ||
+ | |||
+ | Added to both 3.5.2 versions\\ | ||
pycuda\\ | pycuda\\ | ||
--- // | --- // | ||
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* location: / | * location: / | ||
* https:// | * https:// | ||
+ | * biolab (jcoolon, tearley) | ||
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- | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
All of these are located in / | All of these are located in / | ||
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* deepbinner --help | * deepbinner --help | ||
* https:// | * https:// | ||
+ | * fcohanlab (ndelgaudio) | ||
**Canu**: a single molecule sequence assembler for genomes large and small. | **Canu**: a single molecule sequence assembler for genomes large and small. | ||
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* gpu version local to n78 | * gpu version local to n78 | ||
* sample programs / | * sample programs / | ||
+ | * mindlab (ploui et al) | ||
====== FSL ====== | ====== FSL ====== | ||
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* gpu version local on n78 | * gpu version local on n78 | ||
* sample programs / | * sample programs / | ||
+ | * mindlab (ploui et al) | ||
====== Campari ====== | ====== Campari ====== | ||
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* www: https:// | * www: https:// | ||
+ | * astrolab | ||
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* program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
* www: http:// | * www: http:// | ||
+ | * astrolab (kflaherty) | ||
< | < | ||
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* program: see below | * program: see below | ||
* www: http:// | * www: http:// | ||
+ | * astrolab (kflaherty) | ||
< | < | ||
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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 ** | ||
+ | |||
+ | * / | ||
+ | * lmp_mpi-[double-double|single-double|single-single] | ||
+ | * consult this file for packages installed and compilations | ||
+ | * / | ||
+ | * CUDA_ARCH = sm_75 (probably only works on queue exx96) | ||
+ | * sample script in ~hmeij/ | ||
+ | |||
+ | < | ||
+ | |||
+ | # simple colloid example | ||
+ | CPU run -n1 | ||
+ | Performance: | ||
+ | GPU run gpu4=1 double-double: | ||
+ | Performance: | ||
+ | GPU run gpu4=1 single-double: | ||
+ | Performance: | ||
+ | GPU run gpu4=1 single-single: | ||
+ | Performance: | ||
+ | |||
+ | </ | ||
* / | * / | ||
* consult [[cluster: | * consult [[cluster: | ||
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* docs: doc dir inside install_dir, | * docs: doc dir inside install_dir, | ||
* www: http:// | * www: http:// | ||
- | * sample script: | + | * sample script: |
* no gpu capabilitities, | * no gpu capabilitities, | ||
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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 ====== |