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cluster:73 [2021/07/27 19:12] hmeij07 [Miniconda3] |
cluster:73 [2021/08/19 13:03] hmeij07 [Kallisto & Trinity & FastQC] |
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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 ====== | ||
Line 303: | Line 341: | ||
numpy | numpy | ||
time 1.8 h516909a_0 | time 1.8 h516909a_0 | ||
+ | </ | ||
+ | |||
+ | For nwells/ | ||
+ | |||
+ | < | ||
+ | |||
+ | conda install -c schrodinger pymol-bundle | ||
+ | |||
+ | package | ||
+ | ---------------------------|----------------- | ||
+ | apbs-1.5 | ||
+ | biopython-1.78 | ||
+ | bzip2-1.0.8 | ||
+ | collada2gltf-2.1.4 | ||
+ | conda-4.10.3 | ||
+ | curl-7.71.1 | ||
+ | dbus-1.13.18 | ||
+ | expat-2.4.1 | ||
+ | fontconfig-2.13.1 | ||
+ | freemol-1.158 | ||
+ | freetype-2.10.4 | ||
+ | glew-2.0.0 | ||
+ | glib-2.69.0 | ||
+ | gst-plugins-base-1.14.0 | ||
+ | gstreamer-1.14.0 | ||
+ | h5py-2.10.0 | ||
+ | hdf4-4.2.13 | ||
+ | hdf5-1.10.6 | ||
+ | icu-58.2 | ||
+ | jpeg-9d | ||
+ | krb5-1.18.2 | ||
+ | libcurl-7.71.1 | ||
+ | libglu-9.0.0 | ||
+ | libholoplaycore-0.1.0_rc4 | ||
+ | libnetcdf-4.7.4 | ||
+ | libpng-1.6.37 | ||
+ | libssh2-1.9.0 | ||
+ | libtiff-4.0.10 | ||
+ | libuuid-2.32.1 | ||
+ | libxcb-1.13 | ||
+ | libxml2-2.9.10 | ||
+ | lz4-c-1.9.2 | ||
+ | mengine-1 | ||
+ | mpeg_encode-1 | ||
+ | mtz2ccp4_px-1.0 | ||
+ | olefile-0.46 | ||
+ | pcre-8.45 | ||
+ | pdb2pqr-2.1.2+pymol | ||
+ | pillow-6.2.1 | ||
+ | pmw-2.0.1+3 | ||
+ | pthread-stubs-0.4 | ||
+ | pycollada-0.7.1+bdf414c7 | ||
+ | pykerberos-1.2.1 | ||
+ | pymol-2.4.1 | ||
+ | pymol-bundle-2.4.1 | ||
+ | pymol-web-examples-2.4 | ||
+ | pyqt-5.9.2 | ||
+ | qt-5.9.7 | ||
+ | rigimol-1.3 | ||
+ | sip-4.19.13 | ||
+ | xorg-libxau-1.0.9 | ||
+ | xorg-libxdmcp-1.1.3 | ||
+ | zstd-1.4.5 | ||
+ | |||
+ | |||
</ | </ | ||
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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=/ | ||
</ | </ | ||
Line 851: | Line 964: | ||
* location: / | * location: / | ||
* https:// | * https:// | ||
- | * biolab (jcoolon, tearley) | + | |
+ | * queues: hp12, tinymem, mw256fd mw128 | ||
+ | * debug server swallowtail | ||
+ | | ||
Line 861: | Line 977: | ||
< | < | ||
+ | # env | ||
export PATH="/ | export PATH="/ | ||
export LD_LIBRARY_PATH="/ | export LD_LIBRARY_PATH="/ | ||
Line 874: | Line 991: | ||
hdf5 | hdf5 | ||
kallisto | kallisto | ||
+ | |||
+ | |||
+ | # --- // | ||
+ | # Added packages below for Prof Coolon' | ||
+ | |||
+ | |||
+ | conda list | egrep -i " | ||
+ | bedtools | ||
+ | bowtie2 | ||
+ | cufflinks | ||
+ | samtools | ||
</ | </ |