install and launch

[EmmyDx]

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]

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.

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[EmmyDx]

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]

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]

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

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#5 (comment)

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]

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.