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cluster:73 [2021/08/19 12:58] hmeij07 [Kallisto & Trinity & FastQC] |
cluster:73 [2021/09/28 18:27] hmeij07 [Paleogenomics Tools] |
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* centos7 R v 3.6.0 | * centos7 R v 3.6.0 | ||
* use your HPC username and credentials | * use your HPC username and credentials | ||
+ | |||
+ | < | ||
+ | |||
+ | # native OS installation for rstudio | ||
+ | /bin/R | ||
+ | |||
+ | </ | ||
====== DMTCP ===== | ====== DMTCP ===== | ||
Line 634: | Line 641: | ||
</ | </ | ||
- | * https:// | + | |
* The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | * The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. | ||
* requires centos7 (glibc) so queues mwgpu, amber128, exx96 | * requires centos7 (glibc) so queues mwgpu, amber128, exx96 | ||
Line 643: | Line 650: | ||
</ | </ | ||
+ | |||
+ | * **adapterremoval** https:// | ||
+ | * **bwa** https:// | ||
+ | * **bowtie2** http:// | ||
+ | |||
+ | These are all part of Miniconda3 (centos7), to setup the environment consult | ||
+ | |||
+ | * https:// | ||
+ | * queues: mwgpu, amber128, exx96, debug server greentail52 | ||
+ | |||
+ | They are also available via Miniconda2 (centos6), consult | ||
+ | |||
+ | * https:// | ||
+ | * queues: hp12, mw256fd, tinymem, debug server swallowtail | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 ~]$ conda list | egrep " | ||
+ | adapterremoval | ||
+ | bowtie2 | ||
+ | bwa | ||
+ | |||
+ | </ | ||
+ | |||
Line 964: | Line 995: | ||
* location: / | * location: / | ||
* https:// | * https:// | ||
- | * biolab (jcoolon, tearley) | + | |
+ | * queues: hp12, tinymem, mw256fd mw128 | ||
+ | * debug server swallowtail | ||
+ | | ||
Line 974: | Line 1008: | ||
< | < | ||
- | --- // | + | # env |
- | \\ | + | |
- | Added packages below for Prof Coolon' | + | |
- | + | ||
- | < | + | |
- | + | ||
- | conda list | egrep -i " | + | |
- | bedtools | + | |
- | bowtie2 | + | |
- | cufflinks | + | |
- | samtools | + | |
- | + | ||
- | </ | + | |
export PATH="/ | export PATH="/ | ||
export LD_LIBRARY_PATH="/ | export LD_LIBRARY_PATH="/ | ||
Line 1001: | Line 1022: | ||
hdf5 | hdf5 | ||
kallisto | kallisto | ||
+ | |||
+ | |||
+ | # --- // | ||
+ | # Added packages below for Prof Coolon' | ||
+ | |||
+ | |||
+ | conda list | egrep -i " | ||
+ | bedtools | ||
+ | bowtie2 | ||
+ | cufflinks | ||
+ | samtools | ||
</ | </ |