VCRU Bioinformatics - Install notes

This page was last updated on Tuesday, 25-Jun-2019 16:06:09 CDT

Installation notes for Roche 454 software version 3.0

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Prerequisites

To resolve the error message:
Warning: One or more of the following libraries was not found

zlib.i386, libXi.i386, libXtst.i386, libXaw.i386

Without these libraries, 454 Life Sciences software may not
run correctly. Consult the product documentation for more
information.
we need to install 32-bit libraries
1. $ sudo apt-get install lib32z1 lib32ncurses5 lib32bz2-1.0
```
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  libc6-i386
The following NEW packages will be installed:
  lib32z1 libc6-i386
```

Installation

$ ver="3.0"
Contact Roche us.gssupport@roche.com for access to the download page for the software.
I stored it as /programinstallers/Roche3.0/Software_3.0_All_FLX.tgz
$ cd /programinstallers/Roche3.0
Main file is a tarbomb, so
$ mkdir Software_3.0_All_FLX && cd Software_3.0_All_FLX
$ tar -zxvf ../Software_3.0_All_FLX.tgz
We only need DataAnalysis software
$ tar -zxvf DataAnalysis_3.0_All_20140410_1643.tgz
$ cd DataAnalysis_3.0_All
We can only install in an X session
$ sudo ./setup.sh

sudo apt-get install gcc-multilib
[sudo] password for dsenalik: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  gcc-4.8-multilib lib32asan0 lib32atomic1 lib32gcc-4.8-dev lib32gcc1
  lib32gomp1 lib32itm1 lib32quadmath0 libc6-dev-i386 libc6-dev-x32 libc6-x32
  libx32asan0 libx32atomic1 libx32gcc-4.8-dev libx32gcc1 libx32gomp1
  libx32itm1 libx32quadmath0
The following NEW packages will be installed:
  gcc-4.8-multilib gcc-multilib lib32asan0 lib32atomic1 lib32gcc-4.8-dev
  lib32gcc1 lib32gomp1 lib32itm1 lib32quadmath0 libc6-dev-i386 libc6-dev-x32
  libc6-x32 libx32asan0 libx32atomic1 libx32gcc-4.8-dev libx32gcc1 libx32gomp1
  libx32itm1 libx32quadmath0
0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.





sudo -i
cd /etc/apt/sources.list.d
echo "deb http://old-releases.ubuntu.com/ubuntu/ raring main restricted universe multiverse" >ia32-libs-raring.list
apt-get update
apt-get install ia32-libs

Install version 3.0 on ubuntu 16.04.5

$ cd /programinstallers
$ cp -puvr nas/Roche3.0 .
$ cd Roche3.0/Software_3.0_All_FLX/DataAnalysis_3.0_All
This step must be run in an x session
$ sudo ./setup.sh
Two errors, a dialog box "Error: Could not execute command: type rocks 2>&1", and
sh: 1: /sbin/lspci: not found
$ sudo ln -s /usr/bin/lspci /sbin/lspci
If I want to edit the setup.sh file, I need to use
vi -b setup.sh and :set noeol
to avoid corrupting the binary data
$ mkdir bogus; sudo ./setup.sh --keep --nox11 --target bogus --confirmq
$ sudo mv /bin/sh /bin/shokay; sudo ln -s /bin/bash /bin/sh
Warning: One or more of the following libraries was not found
zlib.i386, libXi.i386, libXtst.i386, libXaw.i386
…
$ sudo apt-get install lib32z1 lib32ncurses5 lib32bz2-1.0
however they are all already installed
lib32ncurses5 is already the newest version (6.0+20160213-1ubuntu1).
lib32z1 is already the newest version (1:1.2.8.dfsg-2ubuntu4.1).
lib32bz2-1.0 is already the newest version (1.0.6-5).
$ sudo apt-get install libxi6:i386 libxtst6:i386 libxaw7:i386
I could only do a local install because of the /bin/sh problem, but I was able to install to /opt/454/
Cleanup
$ sudo rm /sbin/lspci
$ sudo rm /bin/sh ; sudo mv /bin/shokay /bin/sh
Create a launcher for all users
$ sudo nano /usr/share/applications/Bioinformatics/gsAssembler.desktop

Add this text:

#!/usr/bin/env xdg-open

[Desktop Entry]
Version=1.0
Type=Application
Terminal=false
Exec=/opt/454/bin/gsAssembler
Path=
Name=gsAssembler 3.0
Comment=
Icon=
Categories=Bioinformatics

Do the same for gsMapper and gsAmplicon
Add to default PATH
$ sudo nano /etc/profile
…
PATH="$PATH:/opt/454/bin"
…