search

wtsi-npg / npg_conda

NPG Conda recipes and tools
1 stars 15 forks source link

Tophat 2.1.1 : patch for C++11 templating #274

Closed dkj closed 3 years ago

dkj commented 3 years ago

Allows use of later base Conda compiler which has correct deps for libraries.

Keeps this last version of Tophat available whilst we should direct such analysis to a more contemporary tool e.g. HISAT2

dkj commented 3 years ago

Some explanation of the template issue (but its application was admittedly somewhat "try it and see"...): https://stackoverflow.com/questions/9641960/c11-make-pair-with-specified-template-parameters-doesnt-compile

dkj commented 3 years ago 
conda create -n testtophat tophat2 libz
Collecting package metadata: done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - tophat2 -> libz
  - libz -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Hmmm...

Update: was using miniconda2 instead of minconda3, seems to work okay with updated conda.

conda create -n testtophat tophat2 libz
  added / updated specs:
    - libz
    - tophat2