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cluster:73 [2021/07/15 17:48] hmeij07 [Sequencing Tools #3] |
cluster:73 [2021/08/19 12:17] hmeij07 [Sequencing Tools #3] |
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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 / | ||
+ | |||
+ | ====== Sequencing Tools #4 ====== | ||
+ | |||
+ | < | ||
+ | |||
+ | libgcc-7.2.0 | ||
+ | samtools-1.7 | ||
+ | |||
+ | </ | ||
====== Sequencing Tools #3 ====== | ====== Sequencing Tools #3 ====== | ||
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192.168.102.251 greentail52-eth0 | 192.168.102.251 greentail52-eth0 | ||
10.10.102.251 | 10.10.102.251 | ||
+ | |||
+ | </ | ||
+ | |||
+ | ** Guppy Client ** | ||
+ | |||
+ | * https:// | ||
+ | * miniconda3 python3.9 | ||
+ | * Python client library for Guppy. | ||
+ | * Full Python client library for communicating with guppy_basecall_server. | ||
+ | * v0.1.0 | ||
+ | |||
+ | < | ||
+ | |||
+ | pip install cython PyUnicode timer | ||
+ | pip install pyguppyclient | ||
+ | Successfully installed flatbuffers-1.11 ont-fast5-api-3.3.0 pyguppyclient-0.0.6 pyzmq-17.1.2 | ||
+ | |||
+ | note: from pyguppyclient import GuppyBasecallerClient, | ||
+ | success, but do not know how to execute the example | ||
</ | </ | ||
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** Due to technical limitations, | ** Due to technical limitations, | ||
+ | |||
+ | < | ||
+ | |||
+ | source / | ||
+ | export PATH=/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | which mpirun python conda | ||
+ | |||
+ | </ | ||
+ | |||
< | < | ||
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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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* Requires CentOS 7 so queues mwgpu, amber128, exx96 | * Requires CentOS 7 so queues mwgpu, amber128, exx96 | ||
+ | * debug node greentail52 | ||
* Production version is installed in / | * Production version is installed in / | ||
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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=/ | ||
</ | </ |