Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix mykrobe python package dependencies #13672

Merged
merged 22 commits into from
Feb 16, 2019
Merged

fix mykrobe python package dependencies #13672

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
22 commits
Select commit Hold shift + click to select a range
1d45b63
update mykrobe to v0.6.1
Feb 8, 2019
ef3e1d6
Update meta.yaml
bgruening Feb 8, 2019
4ad2dae
Merge branch 'master' into mykrobe
bgruening Feb 8, 2019
d60c4cf
add wget to host
bgruening Feb 8, 2019
7d1222a
clean up build script. add test source files
Feb 9, 2019
60bc3cb
Merge branch 'mykrobe' of https://github.com/mbhall88/bioconda-recipe…
Feb 9, 2019
e62adc1
add post-link script for downloading panel data
Feb 9, 2019
5b9dcaf
add prefix location specifier for mykrobe data dir
Feb 11, 2019
29d5178
fix post-link script
Feb 11, 2019
8b44bf5
switch to shasum for data download check. add wget to run reqs
Feb 11, 2019
671d232
use pip install
bgruening Feb 11, 2019
24c5652
Delete build.sh
bgruening Feb 11, 2019
71f57bc
not sure why this has not failed before
bgruening Feb 11, 2019
f43d56f
Update meta.yaml
bgruening Feb 11, 2019
88c6341
fix mccortex install
Feb 14, 2019
d095f5c
use default compiler for cxx
Feb 14, 2019
20a0099
compile with -fPIC
bgruening Feb 14, 2019
98e9dda
remove hard-coded gcc in htslib Makefile. remove unncessary reqs
Feb 14, 2019
2c7ee3d
Merge branch 'mykrobe' of https://github.com/mbhall88/bioconda-recipe…
Feb 14, 2019
fe1aac9
Merge branch 'mykrobe' of https://github.com/mbhall88/bioconda-recipe…
Feb 16, 2019
187d8bf
add python package reqs to run reqs and test
Feb 16, 2019
6d60bf4
Merge branch 'master' into mykrobe
Feb 16, 2019
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions recipes/mykrobe/conda_build_config.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
numpy:
- 1.15
20 changes: 19 additions & 1 deletion recipes/mykrobe/meta.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ source:
md5 : 2650bfab3caa6ac9e142fb19d55f5604

build:
number: 0
number: 1
skip: True # [py27]
entry_points:
- mykrobe = mykrobe.cli:main
Expand All @@ -23,13 +23,31 @@ requirements:
- pip
- zlib
- wget
- numpy
- cython
- mongoengine
- pyvcf
- biopython
run:
- python
- mongodb >3.0
- wget
- zlib
- numpy
- cython
- mongoengine
- pyvcf
- biopython

test:
imports:
- numpy
- cython
- mongoengine
- vcf
- Bio
- mykrobe

commands:
- mykrobe --version
- mykrobe --help
Expand Down