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cluster:73 [2020/06/18 15:31] hmeij07 [Miniconda2] |
cluster:73 [2020/06/18 19:25] hmeij07 |
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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 | ||
< | < | ||
- | 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 | + | |
- | future-0.18.2 | + | export PATH="/ |
- | greenlet-0.4.16 | + | |
- | itsdangerous-1.1.0 | + | export PATH=/ |
- | jinja2-2.11.2 | + | export LD_LIBRARY_PATH=/ |
- | markdown-3.1.1 | + | |
- | monotonic-1.5 | + | which gcc: / |
- | msgpack-python-0.5.6 | + | which python: / |
- | python-engineio-3.13.0 | + | which perl: / |
- | python-socketio-4.6.0 | + | |
+ | 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 | ||
</ | </ | ||
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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) | ||
< | < | ||
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* 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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* 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) | ||
< | < |