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cggh / biipy

Docker image for bioinformatics analysis.
MIT License
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Migrate pip packages to conda #25

Closed hardingnj closed 7 years ago

hardingnj commented 8 years ago

Much faster installation from binary:

anhima == 0.11.2 
ete3 == 3.0.0b29 
fastcluster == 1.1.20 
humanize == 0.5.1 
IntervalTree == 2.1.0 
memory_profiler == 0.41 
openpyxl == 2.3.3 
petl == 1.1.0 
prettypandas == 0.0.2 
py-cpuinfo == 0.1.8 
pymysql == 0.7.1 
pysamstats == 0.24.2 
rpy2 == 2.7.8 
scikit-allel==0.20.3
scikits.bootstrap == 0.3.2 
vcfnp == 2.2.0 
xlwt-future == 0.8.0
zarr == 0.4.0

Some of these ie simuPOP have their own repo (bpeng). Others can be added to a biipy repo or added to bioconda.

Scikit allel has already been moved to conda, so that needs to be changed in biipy.

hardingnj commented 7 years ago

Several of these done. 

anhima == 0.11.2 
ete3 == 3.0.0b29 
fastcluster == 1.1.20 
IntervalTree == 2.1.0 
openpyxl == 2.3.3 
petl == 1.1.0 
prettypandas == 0.0.2 
py-cpuinfo == 0.1.8 
pymysql == 0.7.1 
scikits.bootstrap == 0.3.2 
vcfnp == 2.2.0 
xlwt-future == 0.8.0

remain

alimanfoo commented 7 years ago

I've migrated a few more in #41, think we're at as many as possible now, suggest closing this issue.