cluster:73
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cluster:73 [2020/06/18 15:22] hmeij07 [Matlab] |
cluster:73 [2020/06/18 19:26] hmeij07 [Sequencing Tools #2] |
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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 (tpadillabena) | ||
| + | |||
| + | < | ||
| + | |||
| + | 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 ====== | ||
| Line 23: | Line 68: | ||
| * portainer | * portainer | ||
| * consult [[cluster: | * consult [[cluster: | ||
| + | * QAC | ||
| ====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
| Line 32: | Line 78: | ||
| * BCFtools: | * BCFtools: | ||
| * HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
| + | * Archeology (kbrunson) | ||
| < | < | ||
| Line 79: | Line 126: | ||
| * 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). | ||
| Line 133: | Line 181: | ||
| * 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 ====== | ||
| Line 343: | Line 392: | ||
| * location: / | * location: / | ||
| * https:// | * https:// | ||
| + | * biolab (jcoolon, tearley) | ||
| Line 463: | Line 513: | ||
| - | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
| All of these are located in / | All of these are located in / | ||
| Line 472: | Line 522: | ||
| * 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. | ||
| Line 580: | Line 631: | ||
| * gpu version local to n78 | * gpu version local to n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== FSL ====== | ====== FSL ====== | ||
| Line 589: | Line 641: | ||
| * gpu version local on n78 | * gpu version local on n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== Campari ====== | ====== Campari ====== | ||
| Line 658: | Line 711: | ||
| * www: https:// | * www: https:// | ||
| + | * astrolab | ||
| Line 762: | Line 816: | ||
| * program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 808: | Line 863: | ||
| * program: see below | * program: see below | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07
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