Install: ensure conda-forge in conda channels
General packages have moved from bioconda to conda-forge. Fixes
MODIFY
gemini/gemini_update.py
gemini/gemini_update.py
@@ -19,7 +19,7 @@ def release(parser, args):
if not args.dataonly:
if not os.path.exists(conda_bin):
raise NotImplementedError("Can only upgrade gemini installed with anaconda")
- subprocess.check_call([conda_bin, "install", "-y", "-c", "conda-forget", "-c", "bioconda",
+ subprocess.check_call([conda_bin, "install", "-y", "-c", "conda-forge", "-c", "bioconda",
"gemini", "cyvcf2", "pip"])
if args.devel:
subprocess.check_call([pip_bin, "install", "--upgrade", "--no-deps",

MODIFY
gemini/scripts/gemini_install.py
gemini/scripts/gemini_install.py
@@ -100,7 +100,7 @@ def install_conda_pkgs(anaconda, remotes, args):
else:
req_file = None
pkgs = ["gemini"]
- channels = ["-c", "bioconda"]
+ channels = ["-c", "conda-forge", "-c", "bioconda"]
print(" ".join([anaconda["conda"], "install", "--yes"] + channels + pkgs))
subprocess.check_call([anaconda["conda"], "install", "--yes"] + channels + pkgs)
if req_file and os.path.exists(req_file):

Install: ensure conda-forge in conda channels

General packages have moved from bioconda to conda-forge. Fixes #849