[NicoBxl]

if you want to progress in bioinformatics, go for linux.

There aren't a lot of bioinformatic tools on windows.

[danny0085]

best option

No doubt that the best option is ubuntu linux. Specially for servers

[figure002]

if you want to progress in bioinformatics, go for linux.

There aren't a lot of bioinformatic tools on windows.

No doubt that the best option is ubuntu linux. Specially for servers

I'm an Ubuntu user myself, and Linux would be my first choice as well. But my (former) internship supervisor is a Windows user, and he told me that many of the (bioinformatics) tools he uses are for Windows. But then again, there may be Linux versions or alternatives (I didn't ask which tools he uses exactly).

But if you are right about most bioinformatics tools being available for Linux, than maybe Linux would be a better choice after all.

[GopalJayaraj]

Trouble installing CLC genomics on Ubuntu 12.04

Dear all,

I am new to using NGS analysis tools being a biologist with very limited knowledge about programming. I was browsing about NGS analysis tools which were beginner friendly. I came across CLC genomics workbench and downloaded it onto a Ubuntu workstation (64bit) with 16GB ram. However, the rpm package wont install (inspite of using Alien). The error message i get is the following :

~$ sudo alien CLCGenomicsWorkbench_5_5_2_64.rpm
error: incorrect format: unknown tag
Warning: Skipping conversion of scripts in package CLCGenomicsWorkbench: postinst prerm
Warning: Use the --scripts parameter to include the scripts.
cpio: premature end of file
CLCGenomicsWorkbench_5_5_2_64.rpm is for architecture i386 ; the package cannot be built on this system

I would appreciate if someone guides me through the installation.

Thanks and regards

[lethalfang]

Dear all,

I am new to using NGS analysis tools being a biologist with very limited knowledge about programming. I was browsing about NGS analysis tools which were beginner friendly. I came across CLC genomics workbench and downloaded it onto a Ubuntu workstation (64bit) with 16GB ram. However, the rpm package wont install (inspite of using Alien). The error message i get is the following :

~$ sudo alien CLCGenomicsWorkbench_5_5_2_64.rpm
error: incorrect format: unknown tag
Warning: Skipping conversion of scripts in package CLCGenomicsWorkbench: postinst prerm
Warning: Use the --scripts parameter to include the scripts.
cpio: premature end of file
CLCGenomicsWorkbench_5_5_2_64.rpm is for architecture i386 ; the package cannot be built on this system

I would appreciate if someone guides me through the installation.

Thanks and regards

.rpm works for Redhat based Linux distributions (rpm = redhat package management).
Ubuntu is a Debian based distribution. It needs .deb files, or the installation needs to be built from source.

Edit: Sorry, just noticed that you were using "alien." No experience with that.

[sklages]

Just use the sh installer, not the rpm.

[rivabros]

install CLC on ubuntu with rpm??? Alien did not work

hi, I am having trouble installing clc workbench on an ubuntu 12.04 version.
How do i get the rpm package to install on ubuntu, i tried "alien" and did not work:
error says: wrong architecture, it says clc is a 32 bit, yet i downloaded the 64 bit.
My ubuntu is 64bit.
Thanks for any suggestions!!!
cheers

Hoi figure002,

We run CLC (and more) on an Ubuntu 10.8 x86_64 server with 24 cores and some 47G ram. I am not a CLC user so I can't really give you more details on its performance. People here say that it has trouble with the HiSeq data they feed it because it's just too much, despite the server. They then try to align their reads on one chromosome instead of the entire reference, which I think introduces false positives.

I'd think that the amount of memory is more important than the OS.

Cheers

[sklages]

As I wrote in the previous post: use the sh installer, not the RPM.
And if you have downloaded the installer, it should look like CLCGenomicsWorkbench_6_5_64.sh (with correct version numbers). The final '_64' indicates that this is a 64bit installer ...

[rivabros]

thanks!!!
i did not see the sh installer.

[GenoMax]

The ".sh" installer should be on the same page where you downloaded the rpm installer from. I can see it on a page I get to when I choose "update" from my copy. Both 32- and 64-bit versions are available.

Email tech support at CLC to get the link for a direct download for the .sh installer, if you are a registered user.