cluster:73
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cluster:73 [2023/06/14 18:43] hmeij07 [Miniconda3] |
cluster:73 [2023/07/06 18:21] hmeij07 [Paleogenomics Tools] |
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| Line 346: | Line 346: | ||
| ** Flye ** | ** Flye ** | ||
| - | Somewhat annoying, no miniconda3 package, | + | Somewhat annoying, no miniconda3 package, (python 3.9, gcc 9.2). Local building (without installation) on centos7 greentail52. |
| + | * setup env as for all packages in #3, see top of section | ||
| * v2.9.2 (June 2023) | * v2.9.2 (June 2023) | ||
| * python bin/flye | * python bin/flye | ||
| - | * chnage | + | * change |
| < | < | ||
| Line 384: | Line 385: | ||
| </ | </ | ||
| - | * https:// | ||
| - | * miniconda3 | ||
| - | * De novo assembler for single molecule sequencing reads using repeat graphs | ||
| - | * v2.8.3 | ||
| - | < | ||
| - | |||
| - | # To activate this environment, | ||
| - | # $ conda activate flye | ||
| - | # To deactivate an active environment, | ||
| - | # $ conda deactivate | ||
| - | |||
| - | </ | ||
| ** Filtlong ** | ** Filtlong ** | ||
| Line 1103: | Line 1092: | ||
| pcangsd --version | pcangsd --version | ||
| pcangsd 1.10 | pcangsd 1.10 | ||
| + | |||
| + | </ | ||
| + | |||
| + | * **angsd**, requires miniconda3, same environment as pcangsd | ||
| + | * http:// | ||
| + | * add location of angsd to PATH env | ||
| + | |||
| + | < | ||
| + | |||
| + | $ pwd | ||
| + | / | ||
| + | |||
| + | $ ls -l angsd | ||
| + | -rwxr-xr-x 1 hmeij its 5517248 Jul 6 14:11 angsd | ||
| + | |||
| + | $ ./ | ||
| + | -> angsd version: 0.940-dirty (htslib: 1.16) build(Jul | ||
| </ | </ | ||
| Line 2123: | Line 2129: | ||
| [[https:// | [[https:// | ||
| + | |||
| + | * program v13,2.1 installed | ||
| + | |||
| + | * program v13.2 installed | ||
| * program: mcc, math, mathematica (v 12.2) | * program: mcc, math, mathematica (v 12.2) | ||
| Line 4215: | Line 4225: | ||
| ====== Matlab ====== | ====== Matlab ====== | ||
| + | * installed R2023a | ||
| + | * installed R2022a | ||
| + | |||
| + | * installed R2021a | ||
| * program: Matlab, link to binary is ' | * program: Matlab, link to binary is ' | ||
| Line 4235: | Line 4249: | ||
| ====== Stata ====== | ====== Stata ====== | ||
| + | |||
| + | * program stata[-mp|-se] in your $PATH, version 18 | ||
| + | * v17 will still run so add ' | ||
| + | * so that makes for 12 licenses 8-) | ||
| * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se | * program: Stata v 17, 6-user network license, includes stata, stata-mp, stata-se | ||
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07
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