ubuntu安装只有redhat版本的454分析软件

Posted 2021-04-25 YuLabSMU

各种互X，linux不同发行版X起来就更容易了。两三年前在实验室安装软件的记录，如果重新再让我搞，我可能会搞docker。反正也没人看，我就不翻译了 

互X系列

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.