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 [2021/08/19 12:22] hmeij07 [Sequencing Tools #4] |
cluster:73 [2021/08/30 17:48] hmeij07 [Paleogenomics Tools] |
||
---|---|---|---|
Line 18: | Line 18: | ||
on either cottontail2 or node n33 located at / | on either cottontail2 or node n33 located at / | ||
Some compilations require 7.x and are in / | Some compilations require 7.x and are in / | ||
+ | |||
+ | ====== Miniconda2 ===== | ||
+ | |||
+ | * miniconda2 (python 2.7) is hiding in section | ||
+ | * " | ||
+ | * some packages require centos 6 (like cufflinks) | ||
+ | * many packages are also available in miniconda3 section | ||
+ | * requires centos 7 (python 3.9) | ||
====== Sequencing Tools #4 ====== | ====== Sequencing Tools #4 ====== | ||
+ | |||
+ | Added to miniconda3, see section " | ||
+ | |||
+ | * Requires centos7 so queues mwgpu, amber128, exx96 | ||
+ | * debug server greentail52 | ||
+ | * PREFIX=/ | ||
+ | * python 3.9 | ||
+ | * jcoolon lab | ||
+ | | ||
< | < | ||
Line 35: | Line 52: | ||
bedtools-2.30.0 | bedtools-2.30.0 | ||
+ | # cufflinks requires centos 6, weird, so also added to miniconda2, | ||
+ | # see section " | ||
</ | </ | ||
Line 492: | Line 510: | ||
* 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 616: | 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 625: | Line 650: | ||
</ | </ | ||
+ | |||
+ | * **adapterremoval** https:// | ||
+ | * **bwa** https:// | ||
+ | * **bowtie2** http:// | ||
+ | |||
+ | These are all part of Miniconda3, to setup the environment consult | ||
+ | |||
+ | * https:// | ||
+ | |||
+ | There is also a standalone version of bowtie at | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@greentail52 ~]$ conda list | egrep " | ||
+ | adapterremoval | ||
+ | bowtie2 | ||
+ | bwa | ||
+ | |||
+ | </ | ||
+ | |||
Line 946: | Line 991: | ||
* location: / | * location: / | ||
* https:// | * https:// | ||
- | * biolab (jcoolon, tearley) | + | |
+ | * queues: hp12, tinymem, mw256fd mw128 | ||
+ | * debug server swallowtail | ||
+ | | ||
Line 956: | Line 1004: | ||
< | < | ||
+ | # env | ||
export PATH="/ | export PATH="/ | ||
export LD_LIBRARY_PATH="/ | export LD_LIBRARY_PATH="/ | ||
Line 969: | Line 1018: | ||
hdf5 | hdf5 | ||
kallisto | kallisto | ||
+ | |||
+ | |||
+ | # --- // | ||
+ | # Added packages below for Prof Coolon' | ||
+ | |||
+ | |||
+ | conda list | egrep -i " | ||
+ | bedtools | ||
+ | bowtie2 | ||
+ | cufflinks | ||
+ | samtools | ||
</ | </ |