This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
cluster:73 [2021/11/24 19:05] hmeij07 [EasyBuild] |
cluster:73 [2022/06/28 15:37] hmeij07 [Kallisto & Trinity & FastQC] |
||
---|---|---|---|
Line 3: | Line 3: | ||
====== Software ====== | ====== Software ====== | ||
+ | |||
+ | [[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 19: | Line 24: | ||
Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
+ | |||
+ | ====== HPC SDK ====== | ||
+ | |||
+ | * https:// | ||
+ | * Nvidia SDK v 22.2 | ||
====== Magenta ====== | ====== Magenta ====== | ||
Line 120: | Line 130: | ||
cudatoolkit | cudatoolkit | ||
hoomd | hoomd | ||
+ | |||
+ | |||
+ | # ahh, hamed found an error | ||
+ | conda install -c conda-forge cudatoolkit=10.2 | ||
+ | |||
+ | The following packages will be DOWNGRADED: | ||
+ | |||
+ | cudatoolkit | ||
+ | hoomd 2.9.4-gpu_py38h02d30ca_1 --> 2.9.4-gpu_py38h5bdc439_1 | ||
+ | |||
</ | </ | ||
Line 298: | Line 318: | ||
** Flye ** | ** Flye ** | ||
+ | |||
+ | Somewhat annoying, no miniconda3 package, so local install, use minconda3 env | ||
+ | |||
+ | * v2.9 | ||
+ | * python bin/flye | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | which flye | ||
+ | / | ||
+ | flye --version | ||
+ | 2.9-b1774 | ||
+ | |||
+ | </ | ||
* https:// | * https:// | ||
Line 587: | Line 623: | ||
</ | </ | ||
+ | |||
+ | Added\\ | ||
+ | --- // | ||
+ | # https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | conda install -c bioconda samtools=1.9 --force-reinstall | ||
+ | |||
+ | |||
+ | The following NEW packages will be INSTALLED: | ||
+ | |||
+ | gettext | ||
+ | htslib | ||
+ | libdeflate | ||
+ | libglib | ||
+ | libiconv | ||
+ | |||
+ | The following packages will be UPDATED: | ||
+ | |||
+ | cffi pkgs/ | ||
+ | libedit | ||
+ | samtools | ||
+ | |||
+ | The following packages will be SUPERSEDED by a higher-priority channel: | ||
+ | |||
+ | glib pkgs/ | ||
+ | libffi | ||
+ | ncurses | ||
+ | python | ||
+ | sqlite | ||
+ | |||
+ | $ samtools --version | ||
+ | samtools 1.9 | ||
+ | Using htslib 1.9 | ||
+ | Copyright (C) 2018 Genome Research Ltd. | ||
+ | |||
+ | </ | ||
+ | |||
====== pytraj ====== | ====== pytraj ====== | ||
Line 638: | Line 713: | ||
====== OpenHPC ====== | ====== OpenHPC ====== | ||
- | So I remember where I put the repos ''/ | + | So I remember where I put the tar repo file |
- | * whitetail tar ball for centos7/ | + | * OpenHPC v2.4 |
- | * http:// | + | * Rocky 8.5 |
- | * http://repos.openhpc.community/ohpc-1.3/1.3.9/ | + | * Slurm 20.11.8 |
- | * https://github.com/ | + | * Warewulf 3.9 |
+ | * x86_64 | ||
+ | |||
+ | < | ||
+ | |||
+ | [root@cottontail2 ~]# ll /share/apps/src/cottontail2/ | ||
+ | total 8290421 | ||
+ | -rw------- 1 root root | ||
+ | -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 | ||
+ | |||
+ | </code> | ||
====== OneAPI ====== | ====== OneAPI ====== | ||
Line 854: | Line 940: | ||
</ | </ | ||
+ | * **mapDamage2** | ||
+ | * https:// | ||
+ | * docker container is broke | ||
+ | * requires centos6 so queues hp12, mw128 .. may run elsewhere? | ||
+ | * conda install -c ' | ||
+ | |||
+ | |||
+ | < | ||
+ | |||
+ | # env | ||
+ | export PATH="/ | ||
+ | export LD_LIBRARY_PATH="/ | ||
+ | |||
+ | The following NEW packages will be INSTALLED: | ||
+ | |||
+ | mapdamage2 | ||
+ | pysam bioconda/ | ||
+ | seqtk bioconda/ | ||
+ | |||
+ | [hmeij@petaltail ~]$ mapDamage --version | ||
+ | 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 | ||
+ | |||
+ | </ | ||
Line 1213: | Line 1355: | ||
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. | ||
Line 2948: | Line 3096: | ||
* https:// | * https:// | ||
* C11++ on CentOS6, two version of gcc | * C11++ on CentOS6, two version of gcc | ||
- | * read the R-3.6.1_configure file in ''/ | + | * read the R-3.6.1_configure file in ''/ |
< | < |