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Shintaro Katayama edited this page Apr 13, 2015 · 48 revisions

Installation of prerequisite softwares

This instruction is for the v3dev

For installation of the basal softwares to prepare your (copy of) STRTprep, check the following requirements; but you do not need to install Homebrew or Linuxbrew themselves into your system.

xcode-select --install on your Terminal.app, for easy install of Command Line Tools.

DO NOT UPGRADE/INSTALL the Command Line Tools for Xcode version 6.3, released in April 8th! (why?) Solution is downgrade to the version 6.2 - you can get the old version from Xcode at Apple developer center.

Moreover, you might need more packages as follows.

  • mysql-devel (for kent-tools on CentOS)
  • imake (for openssl on CentOS)
  • python-setuptools (for cmake on CentOS)

Preparation of STRTprep for your project

Then clone STRTprep to your disk with a name as you like - STRTprep3.test for example.

git clone -b v3dev https://github.com/shka/STRTprep.git STRTprep3.test
cd STRTprep3.test

There is an installation script for additional softwares. The script installs Homebrew or Linuxbrew, and more softwares to run analysis within your STRTprep. You need to run it only once when you create the project folder.

bin/install.sh

After the installation, you need to load configuration written in bin/setup.sh as follows, everytime when you would like to proceed tasks within the project folder.

cd STRTprep3.test
. bin/setup.sh

Preparation of bowtie indexes

You need to prepare three indexes for (i) phyX, (ii) genome+spike-in, and (iii) transcriptome. There are scripts to build the indexes.

  1. PhyX index
  • bin/index_phyX.sh; create at src/ebwt/phyX/ref
  1. Genome+spike-in index
  • bin/index_hg19_ercc92_ynbA_u13369.sh; create at src/ebwt/hg19_ercc92_ynbA_u13369/ref
  • bin/index_mm9_ercc92_ynbA_bk000964.sh; create at src/ebwt/mm9_ercc92_ynbA_bk000964/ref
  • bin/index_canFam3_ercc92_ynbA.sh; create at src/ebwt/canFam3_ercc92_ynbA
  • bin/index_susScr3_ercc92_ynbA.sh; create at src/ebwt/susScr3_ercc92_ynbA
  1. Transcriptome index; requires two options - (i) genome version, and (ii) genome+spike-in index
  • bin/index_ensGene.sh; create based on ENSEMBL at src/ebwt/ver_ensGene/ref
  • bin/index_knownGene.sh; create based on UCSC known genes at src/ebwt/ver_knownGene/ref
  • bin/index_refGene.sh; create based on RefSeq at src/ebwt/ver_refGene/ref

The following is an example to build the indexes on hg19 and RefSeq.

. bin/setup.sh
bin/index_phyX.sh
bin/index_index_hg19_ercc92_ynbA_u13369.sh
bin/index_refGene.sh hg19 src/ebwt/hg19_ercc92_ynbA_u13369/ref

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