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cluster:73 [2019/07/23 13:05]
hmeij07 [Python3] 		cluster:73 [2020/02/17 18:02]
hmeij07 [Python3]
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 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
  
 +===== Software =====
  
 The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing). The listings below will be updated as software is installed, location is /share/apps/ or /home/apps/ (same thing).
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 Most of the compilations have been performed by Intel's icc/ifort compilers. Most of the compilations have been performed by Intel's icc/ifort compilers.
  
-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.+Old compilations, mostly located in /share/apps, are RHEL 5.5 \\ 
 +Newer compilations are done with CentOS 6.10 (since summer 2013) \\ 
 +on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ 
 +Some compilations require 7.x and are in /share/apps/CENTOS7 \\ 
 + 
 +====== Paleogenomics Tools ====== 
 + 
 +Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: 
 + 
 +  * http://www.htslib.org/download/ 
 +  * Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format 
 +  * BCFtools:Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants 
 +  * HTSlib: A C library for reading/writing high-throughput sequencing data  
 + 
 +<code> 
 + 
 +# add to environment 
 +export PATH=/share/apps/CENTOS6/samtools/1.10/bin:$PATH 
 +export PATH=/share/apps/CENTOS6/bcftools/1.10.2/bin:$PATH 
 +export PATH=/share/apps/CENTOS6/htslib/1.10.2/bin:$PATH 
 + 
 +</code> 
 + 
 +   * https://github.com/ANGSD/angsd 
 +   * Program for analysing NGS data 
 + 
 +<code> 
 + 
 +# does not seem to work against htslib version above... 
 +export  HTSSRC=/share/apps/CENTOS6/ANGSD/htslib 
 +export PATH=/share/apps/CENTOS6/ANGSD/angsd:$PATH 
 + 
 +</code> 
 + 
 +  * https://www.beast2.org/ 
 +  * BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.  
 + 
 +<code> 
 + 
 +# with local java jre1.8.0_212 
 +export PATH=/share/apps/CENTOS6/beast/2.6.0/bin:$PATH 
 + 
 +</code> 
 + 
 + 
 +====== 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 ====== ====== OpenStructure ======
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 Added to both 3.5.2 versions\\ Added to both 3.5.2 versions\\
 +Successfully installed\\
 +boto-2.49.0 boto3-1.12.0 botocore-1.15.0 gensim-3.8.1 jmespath-0.9.4 s3transfer-0.3.3 smart-open-1.9.0\\
 +joblib, scikit-learn, sklearn\\
 +\\
 +Requirement already satisfied:\\
 +keras keras-preprocessing keras-applications\\
 +tensorflow (requires centos7)\\
 + --- //[[hmeij@wesleyan.edu|Henk]] 2020/02/17 13:02//
 +
 +
 +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//  --- //[[hmeij@wesleyan.edu|Henk]] 2019/07/23 09:04//
  
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 terminado-0.8.2 terminado-0.8.2
 widgetsnbextension-3.5.0 widgetsnbextension-3.5.0
 +json5-0.8.5 
 +jupyterlab-1.0.2 
 +jupyterlab-server-1.0.0 
 +tornado-6.0.3
 </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/3.6.1b/bin:$PATH
 +  export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1b/lib64:$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>
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   * Python 2.7.15   * Python 2.7.15
     * compile with enable-share     * compile with enable-share
-    * numpy and scipy packages+    * numpy and scipy packages, and 
 +    * Successfully installed Send2Trash-1.5.0 backports-abc-0.5 futures-3.3.0 ipaddress-1.0.22  
 +    * ipykernel-4.10.1 jupyter-client-5.3.4 jupyterlab-0.33.12 jupyterlab-launcher-0.11.2  
 +    * notebook-5.7.8 prometheus-client-0.7.1 python-dateutil-2.8.0 singledispatch-3.4.0.3  
 +    * subprocess32-3.5.4 terminado-0.8.2 tornado-5.1.1 
  
 <code> <code>
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 For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page ... For all these installations you will need to set $PATH and $LD_LIBRARY_PATH, look for samples on this page ...
 +
 +  * program: GCC v 9.2.0
 +  * /share/apps/CENTOS6/9.2.0
 +  * note: libgomp disabled for nanopolish compile attempt
 +
 +<code>
 +
 +  wget ftp://ftp.nluug.nl/mirror/languages/gcc/releases/gcc-9.2.0/gcc-9.2.0.tar.gz
 +  tar zxvf gcc-9.2.0.tar.gz
 +  cd gcc-9.2.0
 +  ./contrib/download_prerequisites
 +  ./configure --prefix=/share/apps/CENTOS6/gcc/9.2.0 --disable-libgomp --disable-multilib
 +  make
 +  make install
 +
 +
 +</code>
  
   * program: GCC v 4.8.4   * program: GCC v 4.8.4
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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