conda package for 1.10?

computational-metabolomics / mspurity-galaxy

Galaxy tools for msPurity package: includes precursor ion purity calculations and spectral matching

GNU General Public License v3.0

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conda package for 1.10? #14

Closed bernt-matthias closed 5 years ago

bernt-matthias commented 5 years ago

During installation I get:

PackageNotFoundError: Packages missing in current channels:

  - bioconductor-mspurity 1.10.0*

Tomnl commented 5 years ago

Hi @bernt-matthias

I am currently waiting for the bioconda bioconductor-mspurity release of 1.11.

In the mean time you need to add my personal conda channel "tomnl" to Galaxy, i.e.

Update the galaxy.yml to conda_ensure_channels: tomnl,iuc,conda-forge,bioconda,defaults
Or add --conda_ensure_channels tomnl,iuc,bioconda,conda-forge,defaults to the planemo call

bernt-matthias commented 5 years ago

Installation of the conda package worked, but it seems unusable:

Fatal error: Exit code 1 ()
Loading required package: Rcpp
Error: package or namespace load failed for ?msPurity? in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/gpfs0/home/huberc/R/x86_64-pc-linux-gnu-library/3.4/stringi/libs/stringi.so':
  libicui18n.so.55: cannot open shared object file: No such file or directory
In addition: Warning message:
package ?Rcpp? was built under R version 3.4.3 
Execution halted

bernt-matthias commented 5 years ago

Hmm. That's at least what the galaxy error report of a user says ... If I try to reproduce it libraries load nicely. Have to check this.

bernt-matthias commented 5 years ago

Turns out that the error is due to the interference with a library (stringi) that the user installed in their home.

Tomnl commented 5 years ago

Hi @bernt-matthias

OK, I was having a few issues with conda as well a few weeks back (but unrelated to this I think).

If you still get problems, it might worth remove the current "__biconductor-mspurity" environment from conda completely and install again.

Tomnl commented 5 years ago

Now using bioconductor version 1.12.0