cluster:73
Differences
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| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
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cluster:73 [2020/06/18 18:57] hmeij07 [Sequencing Tools] |
cluster:73 [2020/06/19 17:30] hmeij07 [Python3] |
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| Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
| - | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #2 ====== |
| - | * macs python package | + | * macs python package |
| * http:// | * http:// | ||
| * https:// | * https:// | ||
| * https:// | * https:// | ||
| * https:// | * https:// | ||
| + | * padillalab | ||
| < | < | ||
| Line 28: | Line 29: | ||
| export LD_LIBRARY_PATH="/ | export LD_LIBRARY_PATH="/ | ||
| Successfully installed macs-1.4.3 | 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="/ | ||
| Line 62: | Line 78: | ||
| * portainer | * portainer | ||
| * consult [[cluster: | * consult [[cluster: | ||
| + | * QAC | ||
| ====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
| Line 71: | Line 88: | ||
| * BCFtools: | * BCFtools: | ||
| * HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
| + | * Archeology (kbrunson) | ||
| < | < | ||
| Line 118: | 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). | ||
| Line 172: | Line 191: | ||
| * 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 180: | Line 200: | ||
| ====== Python3 ====== | ====== Python3 ====== | ||
| + | |||
| + | * Python 3.8.3 | ||
| + | * / | ||
| + | * most packages found on this page | ||
| + | * picked up mpirun from miniconda2 apps (that may be a problem) | ||
| Added to both versions\\ | Added to both versions\\ | ||
| Line 382: | Line 407: | ||
| * location: / | * location: / | ||
| * https:// | * https:// | ||
| + | * biolab (jcoolon, tearley) | ||
| Line 502: | Line 528: | ||
| - | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
| All of these are located in / | All of these are located in / | ||
| Line 511: | Line 537: | ||
| * 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 619: | Line 646: | ||
| * gpu version local to n78 | * gpu version local to n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== FSL ====== | ====== FSL ====== | ||
| Line 628: | Line 656: | ||
| * gpu version local on n78 | * gpu version local on n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== Campari ====== | ====== Campari ====== | ||
| Line 697: | Line 726: | ||
| * www: https:// | * www: https:// | ||
| + | * astrolab | ||
| Line 801: | Line 831: | ||
| * program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 847: | Line 878: | ||
| * 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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