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====== Software ====== | ====== Software ====== | ||
- | [[cluster: | + | [[cluster: |
+ | |||
+ | Below is all centos 6 and/or 7, which may or may not run in 8. | ||
IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/ | IMPORTANT NOTE: **Since moving to the TrueNAS/ZFS appliance all references to** ''/ | ||
Line 20: | Line 23: | ||
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 / | ||
+ | |||
+ | |||
+ | |||
+ | ====== Trimmomatic ====== | ||
+ | |||
+ | * http:// | ||
+ | * binary download and stage | ||
+ | * java -jar trimmomatic-0.39.jar ... | ||
+ | |||
+ | < | ||
+ | |||
+ | / | ||
+ | [root@cottontail Trimmomatic-0.39]# | ||
+ | total 176 | ||
+ | drwxr-xr-x 2 root root 8 Apr 8 2019 adapters | ||
+ | -rw-r--r-- 1 root root 35147 May 16 2018 LICENSE | ||
+ | -rw-r--r-- 1 root root 128502 Apr 8 2019 trimmomatic-0.39.jar | ||
+ | |||
+ | </ | ||
Line 220: | Line 242: | ||
Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below). | Suite of tools for high-accuracy basecaling, assembly, polishing, and alignment. Installed in a specific miniconda3 environment (see below). | ||
- | * Requires centos7 so queues mwgpu, amber128, exx96 | + | * Requires centos7 so queues mwgpu, |
* debug server greentail52 | * debug server greentail52 | ||
* PREFIX=/ | * PREFIX=/ | ||
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< | < | ||
- | # environment | + | # environment |
source / | source / | ||
export PATH=/ | export PATH=/ | ||
Line 241: | Line 263: | ||
which conda python pip mpirun gcc cmake | which conda python pip mpirun gcc cmake | ||
python --version | python --version | ||
+ | |||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | / | ||
+ | |||
</ | </ | ||
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** Flye ** | ** Flye ** | ||
+ | |||
+ | Somewhat annoying, no miniconda3 package, so local install, use minconda3 environment as listed top of this section (python 3.9, gcc 9.2) | ||
+ | |||
+ | * v2.9.1 (October 2022) | ||
+ | * python bin/flye | ||
+ | * change the PATHs accordingly | ||
+ | |||
+ | < | ||
+ | |||
+ | / | ||
+ | 2.9.1-b1780 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * v2.9 (August 2021) | ||
+ | * python bin/flye | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | which flye | ||
+ | / | ||
+ | flye --version | ||
+ | 2.9-b1774 | ||
+ | |||
+ | </ | ||
* https:// | * https:// | ||
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Using htslib 1.9 | Using htslib 1.9 | ||
Copyright (C) 2018 Genome Research Ltd. | Copyright (C) 2018 Genome Research Ltd. | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **iqtree** fcohanlab/ | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 ~]$ iqtree --version | ||
+ | IQ-TREE multicore version 2.0.3 for Linux 64-bit built Dec 20 2020 | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | * https:// | ||
+ | * calterlab, annika (used pip to install) | ||
+ | |||
+ | < | ||
+ | |||
+ | Successfully installed | ||
+ | GridDataFormats-1.0.1 MDAnalysis-2.3.0 | ||
+ | fasteners-0.18 mmtf-python-1.1.3 | ||
+ | mrcfile-1.4.3 msgpack-1.0.4 numpy-1.23.4 | ||
</ | </ | ||
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-rw-r--r-- 1 root root 10720 Mar 17 09:35 ohpc-release-2-1.el8.x86_64.rpm | -rw-r--r-- 1 root root 10720 Mar 17 09:35 ohpc-release-2-1.el8.x86_64.rpm | ||
-rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar | -rw-r--r-- 1 root root 8531681280 Mar 17 09:33 OpenHPC-2.4.EL_8.x86_64.tar | ||
+ | |||
+ | |||
+ | |||
+ | # this is all that is needed for ohpc base compute client | ||
+ | # see the recipe for cct2 and follow compute node only ingredients | ||
+ | |||
+ | [root@cottontail2 ~]# ll / | ||
+ | total 95196 | ||
+ | -rw-r--r-- 1 root root 2696360 Feb 10 09:21 hwloc-ohpc-2.7.0-3.9.ohpc.2.6.x86_64.rpm | ||
+ | -rw-r--r-- 1 root root | ||
+ | -rw-r--r-- 1 root root 7268 Feb 10 09:22 ohpc-base-compute-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm | ||
+ | -rw-r--r-- 1 root root 8204 Feb 10 09:23 ohpc-filesystem-2.6-2.3.ohpc.2.6.noarch.rpm | ||
+ | -rw-r--r-- 1 root root 10720 Feb 10 09:23 ohpc-release-2-1.el8.x86_64.rpm | ||
+ | -rw-r--r-- 1 root root 7124 Feb 10 09:27 ohpc-slurm-client-2.6.1-5.1.ohpc.2.6.1.x86_64.rpm | ||
+ | -rw-r--r-- 1 root root 74326532 Feb 10 09:23 singularity-ohpc-3.7.1-5.1.ohpc.2.1.x86_64.rpm | ||
+ | -rw-r--r-- 1 root root 22168 Feb 10 09:24 slurm-contribs-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm | ||
+ | -rw-r--r-- 1 root root | ||
+ | -rw-r--r-- 1 root root 18764472 Feb 10 09:24 slurm-ohpc-22.05.2-14.1.ohpc.2.6.x86_64.rpm | ||
+ | -rw-r--r-- 1 root root | ||
+ | -rw-r--r-- 1 root root | ||
</ | </ | ||
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[hmeij@petaltail ~]$ mapDamage --version | [hmeij@petaltail ~]$ mapDamage --version | ||
2.0.6 | 2.0.6 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **PCAngsd**, | ||
+ | * https:// | ||
+ | * apparently the repo is needed ''/ | ||
+ | |||
+ | < | ||
+ | |||
+ | source / | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | which pcangsd | ||
+ | / | ||
+ | pcangsd --version | ||
+ | pcangsd 1.10 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **Standard RAxML version** | ||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | # add path to $PATH | ||
+ | |||
+ | [hmeij@greentail52 tmp]$ ll / | ||
+ | total 3202 | ||
+ | -rwxr-xr-x 1 hmeij its 1177632 Apr 25 14:49 raxmlHPC-AVX | ||
+ | -rwxr-xr-x 1 hmeij its 1177632 Apr 25 14:49 raxmlHPC-AVX2 | ||
+ | -rwxr-xr-x 1 hmeij its 1152040 Apr 25 14:49 raxmlHPC_serial | ||
+ | -rwxr-xr-x 1 hmeij its 1185704 Apr 25 14:49 raxmlHPC-SSE3 | ||
</ | </ | ||
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cufflinks | cufflinks | ||
samtools | samtools | ||
+ | |||
+ | # fcohan lab | ||
+ | [hmeij@petaltail ~]$ iqtree --version | ||
+ | IQ-TREE multicore version 2.1.4-beta COVID-edition for Linux 64-bit built Jun 24 2021 | ||
</ | </ | ||
+ | |||
+ | |||
**Trinity** assembles transcript sequences from Illumina RNA-Seq data. | **Trinity** assembles transcript sequences from Illumina RNA-Seq data. | ||
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====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** 25Apr2023** | ||
+ | |||
+ | * / | ||
+ | * lmp_serial and lmp_mpi | ||
+ | * 3 cuda versions with 3 different precision settings | ||
+ | * notes: / | ||
+ | |||
+ | < | ||
+ | |||
+ | # CPU | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | which mpirun mpicc python | ||
+ | |||
+ | # CPU + GPU (exx96 queue, may run on test and amber128 queues) | ||
+ | |||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | which nvcc | ||
+ | |||
+ | |||
+ | </ | ||
** USER_QUIP ** | ** USER_QUIP ** | ||
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====== Amber ====== | ====== Amber ====== | ||
+ | |||
+ | ** Amber 22 ** | ||
+ | |||
+ | Details on how to run on CentOS7 can be found at | ||
+ | |||
+ | * https:// | ||
** Amber 20 ** | ** Amber 20 ** |