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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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install and launch #5

Open EmmyDx opened 8 years ago

EmmyDx commented 8 years ago

Dear all; I'm trying to install and launch RetroSeq (using mac os); When I run the command line: perl retroseq.pl -discover -bam file.bam -out ... I obtain this msg: Error: Cant find required binary samtools at retroseq.pl line 195. I've already installed samtools and bedtools (not yet exonerate).

If someone has any idea to solve this problem, I'll be grateful and will try it. Regards E.

tk2 commented 8 years ago

Hi, Is samtools available in your default path? i.e. what happens if you just type 'samtools' on the command line, is it found?

Rgds, Thomas

On 04/04/16 13:32, Emma-Drieux wrote:

Dear all; I'm trying to install and launch RetroSeq (using mac os); When I run the command line: perl retroseq.pl -discover -bam file.bam -out ... I obtain this msg: Error: Cant find required binary samtools at retroseq.pl line 195. I've already installed samtools and bedtools (not yet exonerate).

If someone has any idea to solve this problem, I'll be grateful and will try it. Regards E.

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/wtsi-svi/RetroSeq/issues/5

The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

EmmyDx commented 8 years ago

Dear Thomas, First, thank you for your answer and your help. I've change the path but the version of samtools still not available (I've the last version 1.3). I guess that I'll have the same problem with the other tools (like bedtools). The message I get when I try to use RetroSeq is: ERROR: Cant determine version number of samtools

Do I need to modify the script retroseq.pl? The path I added on my bash_profile is this: export PATH=$PATH:/Users/bioinfo/Programs/samtools-1.3/./samtools

Regards; Emma

EmmyDx commented 8 years ago

Also, to answer to your question, with this path, when I launch samtools (i.e when I type samtools), the tool run correctly; Rgds Emma

tk2 commented 8 years ago

OK, I see your on a Mac. I can't replicate the problem on my linux machine, I'll try to get my hands on a Mac to test on. There is one other problem that you will encounter when we solve this, RetroSeq only works with Samtools up to 0.1.19. I haven't had time to update it to work with >1.0 versions of Samtools yet.

Thomas

On 06/04/16 09:01, Emma-Drieux wrote:

Dear Thomas, First, thank you for your answer and your help. I've change the path but the version of samtools still not available (I've the last version 1.3). I guess that I'll have the same problem with the other tools (like bedtools). The message I get when I try to use RetroSeq is: ERROR: Cant determine version number of samtools

Do I need to modify the script retroseq.pl? The path I added on my bash_profile is this: export PATH=$PATH:/Users/bioinfo/Programs/samtools-1.3/./samtools

Regards; Emma

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/wtsi-svi/RetroSeq/issues/5#issuecomment-206197114

The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

oiiio commented 7 years ago

A bit late here, but if you simply change the "[samtools]" to "[<your path to 0.1.19 binary>/samtools]" in RetroSeq.pl, it should work regardless of Mac/Linux. Had the same 1.3 problem and seems to run this way without trying to have separate global samtools binaries.