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cluster:73 [2021/07/27 19:20] hmeij07 [Miniconda3] |
cluster:73 [2021/08/19 12:53] hmeij07 [Sequencing Tools #4] |
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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 ====== | ||
+ | |||
+ | Added to miniconda3, see section " | ||
+ | |||
+ | * Requires centos7 so queues mwgpu, amber128, exx96 | ||
+ | * debug server greentail52 | ||
+ | * PREFIX=/ | ||
+ | * python 3.9 | ||
+ | * jcoolon lab | ||
+ | | ||
+ | |||
+ | < | ||
+ | |||
+ | # environment | ||
+ | source / | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | |||
+ | libgcc-7.2.0 | ||
+ | samtools-1.7 | ||
+ | bowtie2-2.2.5 | ||
+ | perl-5.26.2 | ||
+ | bedtools-2.30.0 | ||
+ | |||
+ | # cufflinks requires centos 6, weird, so also added to miniconda2, | ||
+ | # see section " | ||
+ | |||
+ | </ | ||
====== Sequencing Tools #3 ====== | ====== Sequencing Tools #3 ====== | ||
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# with local java jre1.8.0_212 | # with local java jre1.8.0_212 | ||
export PATH=/ | export PATH=/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | * https:// | ||
+ | * 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 | ||
+ | |||
+ | < | ||
+ | |||
+ | export PATH=/ | ||
</ | </ |