cluster:73
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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 15:31] hmeij07 [Miniconda2] |
cluster:73 [2020/06/19 16:08] hmeij07 [Sequencing Tools #2] |
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| Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
| - | ====== | + | ====== |
| + | |||
| + | * macs python package (macs2 see below) | ||
| + | * http:// | ||
| + | * https:// | ||
| + | * https:// | ||
| + | * https:// | ||
| + | * padillalab (tpadillabena) | ||
| < | < | ||
| - | Successfully installed | + | export PATH="/ |
| - | MarkupSafe-1.1.1 | + | export LD_LIBRARY_PATH="/ |
| - | Werkzeug-1.0.1 | + | Successfully installed |
| - | bowtie-0.8.1 | + | |
| - | click-7.1.2 | + | # or change python version to |
| - | dnspython-1.16.0 | + | # ls / |
| - | eventlet-0.25.2 | + | / |
| - | flask-1.1.2 | + | |
| - | flask-socketio-4.3.0 | + | # or change python version to |
| - | future-0.18.2 | + | which python: / |
| - | greenlet-0.4.16 | + | pip list: Package |
| - | itsdangerous-1.1.0 | + | --------------- ------- |
| - | jinja2-2.11.2 | + | bowtie |
| - | markdown-3.1.1 | + | MACS2 2.2.7.1 |
| - | monotonic-1.5 | + | numpy 1.18.5 |
| - | msgpack-python-0.5.6 | + | picard |
| - | python-engineio-3.13.0 | + | scipy 1.4.1 |
| - | python-socketio-4.6.0 | + | |
| + | |||
| + | 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 | ||
| </ | </ | ||
| Line 48: | Line 78: | ||
| * portainer | * portainer | ||
| * consult [[cluster: | * consult [[cluster: | ||
| + | * QAC | ||
| ====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
| Line 57: | Line 88: | ||
| * BCFtools: | * BCFtools: | ||
| * HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
| + | * Archeology (kbrunson) | ||
| < | < | ||
| Line 104: | 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 158: | 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 368: | Line 402: | ||
| * location: / | * location: / | ||
| * https:// | * https:// | ||
| + | * biolab (jcoolon, tearley) | ||
| Line 488: | Line 523: | ||
| - | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
| All of these are located in / | All of these are located in / | ||
| Line 497: | Line 532: | ||
| * 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 605: | Line 641: | ||
| * gpu version local to n78 | * gpu version local to n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== FSL ====== | ====== FSL ====== | ||
| Line 614: | Line 651: | ||
| * gpu version local on n78 | * gpu version local on n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== Campari ====== | ====== Campari ====== | ||
| Line 683: | Line 721: | ||
| * www: https:// | * www: https:// | ||
| + | * astrolab | ||
| Line 787: | Line 826: | ||
| * program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 833: | Line 873: | ||
| * program: see below | * program: see below | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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