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getzlab / rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization
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problem with installation #39

Closed kac2053 closed 4 years ago

kac2053 commented 4 years ago

Hi. I downloaded rnaseqc but the command "rnaseqc" does not exist.

I downloaded with the following command: git clone --recursive https://github.com/broadinstitute/rnaseqc.git

And got this in my folder: args.hxx bioio.hpp cloudbuild.yaml Dockerfile LICENSE Makefile Metrics.md python README.md SeqLib src test_data THIRD-PARTY-LICENSES.md

But I didn't see rnaseqc command anywhere in folder or sub-folders. When I try calling rnaseqc command:

$ ./rnaseqc
-bash: ./rnaseqc: No such file or directory

I also tried downloading Git LFS since it's required but when I unzipped and submitted the command git lfs install it said the command didn't exist. I tried git-lfs which is what I see in the folder, it says "cannot execute binary file".

I have CLIP data and ultimately want to plot read coverage across transcripts to see if there is preference for peaks to be at 5'UTR, CDS, or 3'UTR. I think rnaseqc tool will help me get there, like the figure at the bottom of page 11 of manual: https://software.broadinstitute.org/cancer/cga/sites/default/files/data/tools/rnaseqc/RNA-SeQC_Help_v1.1.2.pdf

If rnaseqc won't help me get there, please let me know since this is the reason I want to use it.

Thank you.

agraubert commented 4 years ago

Hello, To produce the binary for rnaseqc in the repo, you'll need to use the Makefile. The command

make

will read the Makefile and attempt to compile rnaseqc for your system. Alternatively, you can download pre-compiled static binaries from the releases page.

agraubert commented 4 years ago

I'm closing this issue as we haven't heard from you in a while. If you still need help feel free to comment and re-open this issue