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tk2 / RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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Compatibility Checks for samtools #9

Closed jfong1123 closed 7 years ago

jfong1123 commented 7 years ago

I have two versions of samtools currently installed, one that is compatible and one that is not. I have put only the correct version on my path and aliased 'samtools' to point to the correct version, but when running Retroseq.pl, it terminates, claiming I am using an incompatible version of samtools.

Is there any way to allow Retroseq to check for the correct version of samtools and run without uninstalling the newer versions of it?

Thanks so much!

tk2 commented 7 years ago

Hi - RetroSeq will use whatever Samtools it finds in the local environment. The alias you set up is not working if RetroSeq is finding the incorrect version. I'm not sure I can help you fixing that.

Rgds, Thomas

On 22/07/16 13:20, jfong1123 wrote:

I have two versions of samtools currently installed, one that is compatible and one that is not. I have put only the correct version on my path and aliased 'samtools' to point to the correct version, but when running Retroseq.pl, it terminates, claiming I am using an incompatible version of samtools.

Is there any way to allow Retroseq to check for the correct version of samtools and run without uninstalling the newer versions of it?

Thanks so much!

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jfong1123 commented 7 years ago

Thanks!

The alias I set up was working from command line, but I think retroseq looks for "samtools" in the "/usr/local/bin/" directory first. Moving other versions of samtools away from the path yields the desired result.