Run Bowtie2 On Linux Tutorial Archive Visit The

Ive been running the local galaxy on a vm, when I try to run markduplicates and AddO.

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Run Bowtie2 On Linux Tutorial Archive Visit The

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I used datamanagerfetchgenomeallfasta to get a galGal4 genome.

I then used datamanagerbowtie2indexbuilder to build bowtie2 index.

I can see the reference genomes and options without a problem.

After I hit run, it seems to go through the bowtie2 process alright as I can see it start and finish in the process monitor, but it can not finish and gave me this error.

Exception: Error Setting BAM Metadata: index: 1: index: samtools: not found.

So I manually add the path to the samtools binary to the system PATH variable and make sure that it can be found on terminal.

Its after the bowtie2 process is finished and when the result is piped to samtools that the error occurs.

While the bowtie2 process itself can locate where samtools is, a python program doesnt seem to be able to.

I then download and build Samtools-1.2 from source.

When Bowtie2 is running, I can see a Samtools running as well.

If I uninstalled the Samtools installed by Galaxy, I cant really start the process at all.

With the automatically installed Samtools, the error shows up apparently after the bowtie2 aligning process is finished.

According to the Job Command-line, the bowtie2 result is piped to samtools.

You should be able to setup a default samtools version and have that sourced through Galaxys dependency resolution systems.

All the error I posted above ( including those following editing binary.py ) all stemmed from this very fact.

Adding the path to samtools to system path variable solves this.

I have added the samtools bin folder (installed along with bowtie2 through the tool shed) to the system PATH but still no luck.

I am still getting an error message almost identical to yours.

Could you try using an older version of samtools (0.1.19) If this solves your issue please report it here.

The galaxy code should then be updated by using pysam.sort and pysam.index ( ).

I solved the problem by installing Samtools to a local directory in the virtual machine.