This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
cluster:73 [2023/10/06 14:57] hmeij07 [Sequencing Tools #3] |
cluster:73 [2024/02/16 11:17] (current) hmeij07 [LAMMPS CPU/GPU] |
||
---|---|---|---|
Line 54: | Line 54: | ||
* thayerlab | * thayerlab | ||
+ | < | ||
+ | |||
+ | # pollacklab | ||
+ | |||
+ | [hmeij@greentail52 ~]$ source / | ||
+ | |||
+ | [hmeij@greentail52 ~]$ conda activate sage | ||
+ | |||
+ | (sage) [hmeij@greentail52 ~]$ sage --version | ||
+ | SageMath version 10.0, Release Date: 2023-05-20 | ||
+ | |||
+ | (sage) [hmeij@greentail52 ~]$ sage | ||
+ | ┌────────────────────────────────────────────────────────────────────┐ | ||
+ | │ SageMath version 10.0, Release Date: 2023-05-20 | ||
+ | │ Using Python 3.11.4. Type " | ||
+ | └────────────────────────────────────────────────────────────────────┘ | ||
+ | |||
+ | sage: exit | ||
+ | (sage) [hmeij@greentail52 ~]$ conda deactivate | ||
+ | [hmeij@greentail52 ~]$ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * **mdtraj, matplotlib, pandas** | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 ~]$ which python | ||
+ | / | ||
+ | | ||
+ | [hmeij@greentail52 ~]$ python | ||
+ | Python 3.11.4 (main, Jul 5 2023, 13:45:01) [GCC 11.2.0] on linux | ||
+ | Type " | ||
+ | >>> | ||
+ | >>> | ||
+ | |||
+ | </ | ||
+ | |||
+ | * ** seaborn** | ||
+ | * https:// | ||
+ | * also in miniconda3/ | ||
+ | |||
+ | < | ||
+ | |||
+ | patsy conda-forge/ | ||
+ | seaborn | ||
+ | seaborn-base | ||
+ | statsmodels | ||
+ | |||
+ | </ | ||
Line 529: | Line 579: | ||
/ | / | ||
+ | [hmeij@greentail52 20231006]$ pwd | ||
+ | / | ||
+ | |||
+ | [hmeij@greentail52 20231006]$ ll bin | ||
+ | total 11448 | ||
+ | -rwxr-xr-x 1 hmeij its | ||
+ | -rwxr-xr-x 1 hmeij its 3823032 Oct 6 15:04 haslr_assemble | ||
+ | -rwxr-xr-x 1 hmeij its 19949 Oct 6 14:48 haslr.py | ||
+ | -rwxr-xr-x 1 hmeij its 20969840 Oct 6 14:59 minia | ||
+ | -rwxr-xr-x 1 hmeij its 23856 Oct 6 15:01 minia_nooverlap | ||
+ | -rwxr-xr-x 1 hmeij its | ||
</ | </ | ||
Line 552: | Line 613: | ||
stLFR_GapCloser [options] | stLFR_GapCloser [options] | ||
... | ... | ||
+ | |||
+ | |||
+ | # and another request by Luis | ||
+ | # https:// | ||
+ | |||
+ | [hmeij@greentail52 stLFR]$ pwd | ||
+ | / | ||
+ | [hmeij@greentail52 stLFR]$ ll GapCloser-bin-v1.12-r6/ | ||
+ | total 175 | ||
+ | -rwxr-xr-x 1 hmeij its 184713 Jan 11 2013 GapCloser | ||
+ | -rw-r--r-- 1 hmeij its 44533 Jan 11 2013 GapCloser_Manual.pdf | ||
+ | |||
</ | </ | ||
+ | ** BUSCO ** | ||
+ | |||
+ | * https:// | ||
+ | * conda package fails on glib 2.17, weird | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@n79 ~]$ docker images | ||
+ | REPOSITORY | ||
+ | ezlabgva/ | ||
+ | |||
+ | |||
+ | [hmeij@n79 busco_wd]$ docker run --rm -v $(pwd):/ | ||
+ | 2023-10-28 20:30:00 INFO: ***** Start a BUSCO v5.5.0 analysis, current time: 10/28/2023 20:30:00 ***** | ||
+ | 2023-10-28 20:30:00 INFO: | ||
+ | 2023-10-28 20:30:00 INFO: Mode is genome | ||
+ | 2023-10-28 20:30:00 INFO: ' | ||
+ | 2023-10-28 20:30:00 INFO: | ||
+ | |||
+ | that's a problem, trying to reach the internet ... | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** picard ** | ||
+ | |||
+ | * https:// | ||
+ | * Warning: using Java 20 but only Java 17 has been tested. | ||
+ | |||
+ | < | ||
+ | |||
+ | picard centos7, weird | ||
+ | > Failed to load native library ' | ||
+ | |||
+ | picard centos8 | ||
+ | |||
+ | [hmeij@cottontail2 20231108]$ pwd | ||
+ | / | ||
+ | |||
+ | [hmeij@cottontail2 20231108]$ ls -l build/libs/ | ||
+ | total 119872 | ||
+ | -rw-r--r-- 1 hmeij its 62520451 Nov 8 11:46 picard-3.1.0-3-ga9194bd97-SNAPSHOT-all.jar | ||
+ | -rw-r--r-- 1 hmeij its 1856980 Nov 8 11:01 picard-3.1.0-3-ga9194bd97-SNAPSHOT.jar | ||
+ | -rw-r--r-- 1 hmeij its 62520451 Nov 8 11:46 picard.jar | ||
+ | [hmeij@cottontail2 20231108]$ | ||
+ | |||
+ | |||
+ | </ | ||
====== Galario CPU+GPU ====== | ====== Galario CPU+GPU ====== | ||
Line 1264: | Line 1384: | ||
</ | </ | ||
+ | |||
+ | |||
+ | * **qualimap ** | ||
+ | * http:// | ||
+ | * java & R app, probably will work in centos7 and rocky8 | ||
+ | * / | ||
+ | |||
+ | * **gatk** | ||
+ | * https:// | ||
+ | * java & R app. probably will work in centos7 and rocky8 | ||
+ | * / | ||
+ | |||
+ | For both apps above java is v20, developers want and tested v17 | ||
+ | |||
+ | For both apps you may find R local in operating system or a recent versions at | ||
+ | |||
+ | * (rocky 8) module load R/4.1.2 | ||
+ | |||
+ | |||
+ | |||
Line 2467: | Line 2607: | ||
====== LAMMPS CPU/GPU ====== | ====== LAMMPS CPU/GPU ====== | ||
+ | |||
+ | ** 7Feb2024 ** | ||
+ | |||
+ | |||
+ | * / | ||
+ | * lmp_serial and lmp_mpi | ||
+ | * 3 cuda versions with 3 different precision settings | ||
+ | * compiled against cuda 10.2 on exx96, may work in mwgpu cuda-11.2 | ||
+ | * notes: / | ||
+ | * does **not** support openmp, look for the OpenHPC version for that | ||
** 25Apr2023** | ** 25Apr2023** |