install 454 GS Data Analysis Software on ubuntu
Usually Roche’s installer is a catastrophe, they only provides rpm
packages of the software for 454 GS FLX (version 2.9).
Although the package contains setup.sh, the script is useless since it
is actually a binary payload.
I run the setup.sh, and it throw error of not finding /sbin/lspci
. In
debian derived distribution, lspci command is located in /bin folder.
This issue is easy to solve by adding a soft link to /sbin/lspci
.
The second error message popping up says: "Error: Could not execute
command: type rocks 2>&1"
, and I used the command, sudo ln -s
/bin/true /bin/rocks, to solve it.
The third error is lack of libraries zlib.i386
, libXi.i386
,
libXtst.i386
, and libXaw.i386
. Since my OS is 64bit ubuntu 14.04 LTS, I
used, sudo apt-get install ia32-libs
, to install all the 32bit
compatible libraries.
The fourth error is weird for it can’t found /bin/sh
which is available
for all unix-like systems. Since debian links sh to dash, while most of
the Linux distributions links to bash, I changed the link to bash but
the error still exists.
I can’t figure out how to solve the fourth error and tried to install
the rpm packages by using rpm -ivh
command but the error doesn’t change.
Although I can’t install the software using setup.sh, it install java6
successfully. I do believe I can install the software since it is java
program. I start to extract the contents of these rpm packages and then
it is very clear. Some programs, mostly tools of gsSeqTools
, are binary
files that needs shared libs and it is the reason why it throw error of
lacking libraries. This issue had been solved.
Most of the programs are jar files, and shell scripts that wrap the calling of these jar files. All these jar and shell script files can run properly by copying them to the right place.
The contents of rpm file can be extracted using the command like:
rpm2cpio gsAmplicons-2.9-1.noarch.rpm| cpio -idmv
This is the key point of successfully installing 454 GS Data Analysis Software. I believe it can be installed on most of the Unix-like system.
update
When I upgrade Ubuntu to 16.04, I found that ia-32 is no more exist in package repo.
So, we need to download corresponding old packages:
- http://launchpadlibrarian.net/105344356/ia32-libs-multiarch_20090808ubuntu36_i386.deb
- http://mirrors.kernel.org/ubuntu/pool/universe/i/ia32-libs/ia32-libs_20090808ubuntu36_amd64.deb
Then, use sudo dpkg --force-all -i
to install them and sudo apt-get install -f --fix-missing
to install corresponding i386
packages.