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cluster:73 [2022/04/01 14:13] hmeij07 [Paleogenomics Tools] |
cluster:73 [2022/04/25 18:52] hmeij07 [Paleogenomics Tools] |
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====== 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 313: | 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 922: | Line 943: | ||
* https:// | * https:// | ||
* docker container is broke | * docker container is broke | ||
- | * requires centos6 so queues hp12, mw128 | + | * requires centos6 so queues hp12, mw128 .. may run elsewhere? |
* conda install -c ' | * conda install -c ' | ||
Line 940: | Line 961: | ||
[hmeij@petaltail ~]$ mapDamage --version | [hmeij@petaltail ~]$ mapDamage --version | ||
2.0.6 | 2.0.6 | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **PCAngsd**, | ||
+ | * https:// | ||
+ | |||
+ | < | ||
+ | |||
+ | 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 | ||
</ | </ |