TAMrS: does the program install properly on non Ubuntu Linux?

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Is there anybody out there– running a Linux distro other than Ubuntu– can you download and install some new software I’m writing. I want to make sure it works on other Linux distros..

The software pipeline aims to drastically simplify transcriptome assembly- input PE or SE fastQ files, out pops an assembly and estimates of expression.

5 minutes: tops (assuming you have Trinity/BWA/samTools installed and in your $PATH..)

wget https://downloads.sourceforge.net/project/tamrs/TAMrS-v0.0.4.tgz
tar -zxf TAMrS-v0.0.4.tgz
cd tamrs-code/
make check         #runs v. small test dataset, <3 minutes
more unit_test/run.map.stats

This should give you something like:

20037 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
4596 + 0 mapped (22.94%:-nan%)
20037 + 0 paired in sequencing
10022 + 0 read1
10015 + 0 read2
3812 + 0 properly paired (19.02%:-nan%)
4031 + 0 with itself and mate mapped
565 + 0 singletons (2.82%:-nan%)
2823 + 0 with mate mapped to a different chr
1393 + 0 with mate mapped to a different chr (mapQ>=5)



  • Matt MacManes

    Seems to fail on Open Suse at the Trinity stage: I wonder if this is a Java issue

  • Peter Fields

    I don’t think it’s a java issue in this case. Though the initial check suggests samtools are found, the text within the log files says:

    Error, cannot find samtools. Please be sure samtools is installed and included in your PATH setting.

    I will fix this and try again.

  • Peter Fields

    That did it! I got roughly the same output as above.

    • Matt MacManes

      awesome! Thanks

  • Scott R. Santos


    TAMrS deployment went fine in Scientific Linux 6.4 (a RHEL clone similar to CentOS) with:


    Nice work and looking forward to comparing this pipeline to our current one.

    • Matt MacManes

      Great to hear. Please do let me know how it compares- both in making the process easy as well as the actual quality of the assembly.