cluster:73
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cluster:73 [2020/06/18 15:34] hmeij07 [Miniconda2] |
cluster:73 [2020/07/31 19:10] hmeij07 |
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| ====== Software ====== | ====== Software ====== | ||
| + | ** | ||
| + | IMPORTANT NOTE: Since moving to the TrueNAS/ZFS appliance all references to ''/ | ||
| + | |||
| + | --- // | ||
| The listings below will be updated as software is installed, location is / | The listings below will be updated as software is installed, location is / | ||
| Line 15: | Line 19: | ||
| Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
| - | ====== | + | ====== |
| + | |||
| + | * / | ||
| + | * / | ||
| + | * https:// | ||
| + | * jfabry/ | ||
| + | |||
| + | ====== Sequencing Tools #2 ====== | ||
| + | |||
| + | * macs python package (macs2 see below) | ||
| + | * http:// | ||
| + | * https:// | ||
| + | * https:// | ||
| + | * https:// | ||
| + | * padillalab | ||
| < | < | ||
| Line 21: | Line 39: | ||
| export PATH="/ | export PATH="/ | ||
| export LD_LIBRARY_PATH="/ | export LD_LIBRARY_PATH="/ | ||
| - | export PATH="/ | + | Successfully installed macs-1.4.3 # note: macs2 Python version must >= 3.6! |
| - | export PATH="/ | + | |
| - | export PATH="/ | + | |
| - | export PATH="/ | + | |
| - | export LD_LIBRARY_PATH="/ | + | |
| - | Successfully installed | + | # or change python version to |
| - | MarkupSafe-1.1.1 | + | # ls / |
| - | Werkzeug-1.0.1 | + | / |
| - | bowtie-0.8.1 | + | |
| - | click-7.1.2 | + | # or change python version to |
| - | dnspython-1.16.0 | + | which python: / |
| - | eventlet-0.25.2 | + | pip list: Package |
| - | flask-1.1.2 | + | --------------- ------- |
| - | flask-socketio-4.3.0 | + | bowtie |
| - | future-0.18.2 | + | MACS2 2.2.7.1 |
| - | greenlet-0.4.16 | + | numpy 1.18.5 |
| - | itsdangerous-1.1.0 | + | picard |
| - | jinja2-2.11.2 | + | scipy 1.4.1 |
| - | markdown-3.1.1 | + | |
| - | monotonic-1.5 | + | |
| - | msgpack-python-0.5.6 | + | export PATH="/ |
| - | python-engineio-3.13.0 | + | |
| - | python-socketio-4.6.0 | + | 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 56: | Line 89: | ||
| * portainer | * portainer | ||
| * consult [[cluster: | * consult [[cluster: | ||
| + | * QAC | ||
| ====== Paleogenomics Tools ====== | ====== Paleogenomics Tools ====== | ||
| Line 65: | Line 99: | ||
| * BCFtools: | * BCFtools: | ||
| * HTSlib: A C library for reading/ | * HTSlib: A C library for reading/ | ||
| + | * Archeology (kbrunson) | ||
| < | < | ||
| Line 112: | Line 147: | ||
| * 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 166: | Line 202: | ||
| * 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 175: | Line 212: | ||
| ====== 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) | ||
| + | |||
| + | < | ||
| + | |||
| + | # needed for _ctypes to compile properly for https retrievals | ||
| + | yum install openssl openssl-devel | ||
| + | yum install yum install libffi-devel libffi | ||
| + | |||
| + | tar -xvf ../ | ||
| + | cd Python-3.8.3/ | ||
| + | ./configure --prefix=/ | ||
| + | make | ||
| + | make install | ||
| + | pip3 install --upgrade pip | ||
| + | # make symbolic links python3-> | ||
| + | # drop all the packages in from previous versions | ||
| + | https:// | ||
| + | |||
| + | </ | ||
| + | |||
| + | |||
| + | Added to both 3.5.2 versions\\ | ||
| pycuda\\ | pycuda\\ | ||
| --- // | --- // | ||
| Line 376: | Line 437: | ||
| * location: / | * location: / | ||
| * https:// | * https:// | ||
| + | * biolab (jcoolon, tearley) | ||
| Line 496: | Line 558: | ||
| - | ====== Sequencing Tools ====== | + | ====== Sequencing Tools #1 ====== |
| All of these are located in / | All of these are located in / | ||
| Line 505: | Line 567: | ||
| * 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 613: | Line 676: | ||
| * gpu version local to n78 | * gpu version local to n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== FSL ====== | ====== FSL ====== | ||
| Line 622: | Line 686: | ||
| * gpu version local on n78 | * gpu version local on n78 | ||
| * sample programs / | * sample programs / | ||
| + | * mindlab (ploui et al) | ||
| ====== Campari ====== | ====== Campari ====== | ||
| Line 691: | Line 756: | ||
| * www: https:// | * www: https:// | ||
| + | * astrolab | ||
| Line 795: | Line 861: | ||
| * program: see below, binary download, no requirement checks. | * program: see below, binary download, no requirement checks. | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 841: | Line 908: | ||
| * program: see below | * program: see below | ||
| * www: http:// | * www: http:// | ||
| + | * astrolab (kflaherty) | ||
| < | < | ||
| Line 886: | Line 954: | ||
| ====== Gromacs ===== | ====== Gromacs ===== | ||
| + | |||
| + | Gromacs-2020.3 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * see / | ||
| + | * change env in script below | ||
| + | |||
| + | Gromacs-2018 for GPU (RTX2080S) | ||
| + | * '' | ||
| + | * **/ | ||
| Line 993: | Line 1070: | ||
| [[https:// | [[https:// | ||
| - | * program: mcc, math, mathematica (v 11.0.1) | + | * program: mcc, math, mathematica (v 12.1) |
| - | * install dir: / | + | * install dir: / |
| * docs: on the web | * docs: on the web | ||
| * www: http:// | * www: http:// | ||
| + | * Campus wide license, use any queue. | ||
| * Parallel kernels | * Parallel kernels | ||
| Line 1003: | Line 1081: | ||
| * http:// | * http:// | ||
| - | Job submissions should go to queue // | + | |
| ====== Eigen ===== | ====== Eigen ===== | ||
| Line 1187: | Line 1265: | ||
| ====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
| + | |||
| + | ** CPU ONLY v2 CentOS7 ** | ||
| + | |||
| + | * add user-opm on next compile ... done ... binaries with string +user-omp | ||
| + | * / | ||
| + | * lmp_serial, lmp_mpi | ||
| + | * //latest// openmpi version as of today v4.0.4 | ||
| + | * consult this file for packages installed and compilations | ||
| + | * / | ||
| + | * should work only on exx96 and mwgpu queues | ||
| + | |||
| + | < | ||
| + | | ||
| + | | ||
| + | </ | ||
| ** CPU ONLY ** | ** CPU ONLY ** | ||
| Line 1199: | Line 1292: | ||
| ** CPU or GPU ** | ** CPU or GPU ** | ||
| + | |||
| + | * added lmp_mpi-single-single+user-omp | ||
| * / | * / | ||
| Line 1205: | Line 1300: | ||
| * / | * / | ||
| * CUDA_ARCH = sm_75 (probably only works on queue exx96) | * CUDA_ARCH = sm_75 (probably only works on queue exx96) | ||
| - | * sample script in ~hmeij/ | + | |
| < | < | ||
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07
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