Problem with installation enviroment and importing BamTools module - missing compiler?

[stewalsh04]

We tried installing the code from cgat-developers using the install-devel.sh

We did this I tried to go into the cgat-flow folder and switch to a remote branch, however the downloaded cgat code repositories core, apps, flow did not seem to be linked to git

(cgat-proj078) [stevenw@cgat050 4_peakcalling]$ git status fatal: not a git repository (or any parent up to mount point /ifs) Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).

I deleted them and cloned them directly from git using ssh. in each of the cgat code repositories I then ran python setup.py develop in cgat-core, cgat-apps and cgat-flow however then got import errors when trying to run pipeline_peakcalling.py

ModuleNotFoundError: No module named 'cgat.BamTools.bamtools'Traceback (most recent call last): File "/ifs/projects/stevenw/cgat/cgat-flow/cgatpipelines/tools/pipeline_peakcalling.py", line 252, in import cgatpipelines.tasks.mappingqc as mappingqc

We think this was because there might have been a missing compiler in the cgat-flow enviroment?

Creating a new conda enviroment from @Charlie-George working cgat-f enviroment, switching to this and then running python setup.py develop in the cgat-core, cgat-apps and cgat-flow directories seemed to fix it ....

[Acribbs]

This is most likely due to either the c compilers not being installed or a conda version that hasn't been packaged correctly (I am finding that there are quite a lot of these problems).

I have had significant issues with the fact that some packages are no longer pinned (specifically the r and bioconductor packages in bioconda and a few conflicts with installing emacs though conda). I think this is because some conda versions of the software aren't properly packaged and sebastian performed quite a lot of testing to make sure all the environment works properly. I think @AndreasHeger is still working on the environment but from my perspective, the installation script worked and now it doesn't. I wonder if in the mean time you can upload the conda environment yml from @Charlie-George so we can use this in the meantime?

[Charlie-George]

Attached is my current cgat-flow env - there are a few extra's that I've added (mainly atac-seq related so feel free to take them out if needs be)

full_cgat_env_dec18.txt

[Acribbs]

Awesome, thanks @Charlie-George