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cluster:73 [2019/07/17 17:11]
hmeij07 [Python2] 		cluster:73 [2019/10/02 14:31]
hmeij07 [OpenStructure]
Line 11: Line 11:
  
 The list of software was primarily compiled under RHEL5.1 but more recent compilation are done on host sharptail under RHEL5.5. Newer compilations are done with CentOS 6.5 (since summer 2013) on either swallowtail or node n33. The list of software was primarily compiled under RHEL5.1 but more recent compilation are done on host sharptail under RHEL5.5. Newer compilations are done with CentOS 6.5 (since summer 2013) on either swallowtail or node n33.
 +
 +====== CD-HIT ======
 +
 +CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. 
 +
 +  * https://github.com/weizhongli/cdhit/wiki
 +  * /share/apps/CENTOS6/cd-hit-v4.8.1-2019-0228/
 +
 +
 +====== OpenStructure ======
 +
 +Open-Source Computational Structural Biology Framework
 +
 +  * v 1.9
 +  * https://openstructure.org/
 +  * recipe at /share/apps/CENTOS6/openstructure/1.9-install.txt
 +
 +OpenStructure relies on these applications and Python 2.7.15 (see python2 section).
 +
 +<code>
 +
 +-- Boost version: 1.68.0
 +-- Found the following Boost libraries:
 +--   python
 +--   unit_test_framework
 +--   filesystem
 +--   system
 +--   iostreams
 +--   program_options
 +--   regex
 +--   thread
 +-- Found ZLIB: /share/apps/CENTOS6/zlib/1.2.11/lib/libz.so (found version "1.2.11")
 +-- Found PNG: /share/apps/CENTOS6/lpng/1.6.37/lib/libpng.so (found version "1.2.49")
 +-- Found EIGEN: /share/apps/CENTOS6/eigen/3.2.10
 +-- Numpy headers found
 +-- Found FFTW: /share/apps/CENTOS6/fftw/3.3.8-enable-single/lib/libfftw3f.so
 +-- Found TIFF: /share/apps/CENTOS6/tiff/4.0.9/lib/libtiff.so (found version "4.0.9")
 +
 +
 +# setup the environment
 +egrep ^export /share/apps/CENTOS6/openstructure/1.9-install.txt
 +
 +ost --help
 +Usage:
 +
 +    ost [ost options] [script to execute] [script parameters]
 +
 +or
 +    ost [action name] [action options]
 +
 +
 +</code>
 +
 +Remarkably complex compilations.
 +
  
 ====== PyCharm EDU ====== ====== PyCharm EDU ======
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   * add the bin/ directory to your PATH (see examples on this page)   * add the bin/ directory to your PATH (see examples on this page)
   * http://abacus.gene.ucl.ac.uk/software/paml.html   * http://abacus.gene.ucl.ac.uk/software/paml.html
 +
 +====== Spyder ======
 +
 +  * Spyder: The Scientific Python Development Environment 
 +  * https://docs.spyder-ide.org/index.html
 +  * See Python 3.5.2 for more details
  
 ====== Python3 ====== ====== Python3 ======
  
- --- //[[hmeij@wesleyan.edu|Henk]] 2019/04/25 09:21//+Added to both 3.5.2 versions\\ 
 +''jupyter-notebook'' only runs in 3.5.2 (non-mpi)\\ 
 + --- //[[hmeij@wesleyan.edu|Henk]] 2019/07/23 09:04//
  
-Added to both python versions 3.5.2 and 3.5.2-mpi the following modules all needed for Spyder.+<code> 
 +Successfully installed 
 +Send2Trash-1.5.0 
 +ipywidgets-7.5.0 
 +jupyter-1.0.0 
 +jupyter-client-5.3.1 
 +jupyter-console-6.0.0 
 +notebook-6.0.0 
 +prometheus-client-0.7.1 
 +terminado-0.8.2 
 +widgetsnbextension-3.5.0 
 +json5-0.8.5  
 +jupyterlab-1.0.2  
 +jupyterlab-server-1.0.0  
 +tornado-6.0.3 
 +</code> 
 + 
 + 
 + 
 +Added to both python versions 3.5.2 and 3.5.2-mpi the following modules all needed for Spyder.\\ 
 + --- //[[hmeij@wesleyan.edu|Henk]] 2019/04/25 09:21//
  
-  * Spyder: The Scientific Python Development Environment  
-  * https://docs.spyder-ide.org/index.html 
  
 <code> <code>
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   * www: http://www.python.org/   * www: http://www.python.org/
  
-====== Kallisto & Trinity ======+====== Kallisto & Trinity & FastQC====== 
 + 
 +**FastQC** A quality control tool for high throughput sequence data. 
 + 
 +  * ''java -version'' latest JDK installed, in default PATH ''which java'' 
 +  * location: /share/apps/FastQC/0.11.8 
 +  * https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 
  
 **kallisto** is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. **kallisto** is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
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 </code> </code>
 +
 +
  
  
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 ====== R & R/parallel ====== ====== R & R/parallel ======
  
 +  * R 3.6.1 (running against "packages", had to comment out libcurl version check)
 +  * New java jdk-12.0.2 (by default in your path)
 +  * packages lme4 and tidyverse installed (dependencies=TRUE)
 +  * https://www.r-bloggers.com/what-are-the-best-machine-learning-packages-in-r/
 +  * packages: mice, rpart, party, caret, randomforest, nnet, e1071, kernLab, xgboost
 +    * note: had to make a link to omp.h from gcc 4.8.4 to OS native gcc...works?
 +
 +<code>
 +
 +  export PATH=/share/apps/CENTOS6/R/packages/bin:$PATH
 +  export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH
 +  export PATH=/share/apps/CENTOS6/R/3.6.1/bin:$PATH
 +  export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1/lib64:$LD_LIBRARY_PATH
 +  export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH
 +  export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH
 +
 +  #export PATH=/share/apps/java/jdk-12.0.2/bin:$PATH
 +  #export LD_LIBRARY_PATH=/share/apps/java/jdk-12.0.2/lib:$LD_LIBRARY_PATH
 +
 +</code>
  
   * R 3.5.1 (new libcurl package)   * R 3.5.1 (new libcurl package)
-  * Uses same old java home 1.7.0_21, should remember to update+  * Uses same old java home 1.7.0_21 (jdk or jre?), should remember to update
   * package lme4 installed   * package lme4 installed
  
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 export PATH=/home/apps/CENTOS6/R/3.5.1/bin:$PATH export PATH=/home/apps/CENTOS6/R/3.5.1/bin:$PATH
 export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/3.5.1/lib64:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/3.5.1/lib64:$LD_LIBRARY_PATH
 +
 +export PATH=/share/apps/java/jdk1.7.0_21/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/java/jdk1.7.0_21/lib:$LD_LIBRARY_PATH
  
 </code> </code>
Line 2268: Line 2381:
 <code> <code>
  
-export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH                                                                +export PATH=/share/apps/CENTOS6/python/2.7.15/bin:$PATH
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.15/lib:$LD_LIBRARY_PATH
  
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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