I'm working from the Biostar Handbook and trying to do the alignment with tophat. I'm on page 480 for reference.
I was able to successfully run
$ bowtie2-build $REF $IDX
However, then it says that I need to change the invocation of the aligner to
$ tophat -G $GTF -o tophat_hbr1 $IDX $R1 $R2 bash: /usr/bin/tophat: No such file or directory (bioinfo)
And that's my output. If I do which tophat, nothing comes up, so it seems like it's just not there. So, I tried to install tophat with
$ conda install tophat Fetching package metadata ................. Solving package specifications: . UnsatisfiableError: The following specifications were found to be in conflict: - python 3.6* - tophat -> python 2.7* Use "conda info <package>" to see the dependencies for each package. (bioinfo)
I saw some solutions online for changing a line of code in tophat to do this, but I don't even know where that file is. I can downgrade python, but I'm not sure if that will work, and I'm worried that I'll break other things if I do. Also, when I do
$ ls /usr/bin | grep python dh_python2 dh_python3 python python-config python2 python2-config python2.7 python2.7-config python3 python3.4 python3.4m python3m x86_64-linux-gnu-python-config x86_64-linux-gnu-python2.7-config (bioinfo) moltres@moltres-ao ~/biostar/Sequencing/griffith $ python -V Python 3.6.3 (bioinfo)
I see a bunch of different python versions, and I'm not sure if I should switch between them or what.
I'm a little frustrated because I bought this book because I'm a beginner, but I keep running into errors that are over my head. I'd really appreciate help here.