diff --git a/bin/gctree-run.py b/bin/gctree-run.py index 3ad9e7e06..9d5f7d256 100755 --- a/bin/gctree-run.py +++ b/bin/gctree-run.py @@ -47,10 +47,10 @@ def idfn(): def install(): cmds = ['#!/bin/bash'] cmds += utils.mamba_cmds(args.env_label, only_prep=True) - cmds += ['micromamba create -n %s -c conda-forge python=3.9' % args.env_label] # 3.10 currently has problems with ete + cmds += ['micromamba create -y -n %s -c conda-forge python=3.9' % args.env_label] # 3.10 currently has problems with ete cmds += ['micromamba activate %s' % args.env_label] - cmds += ['micromamba install -c bioconda -c conda-forge phylip'] - cmds += ['micromamba install -c conda-forge%s click' % ('' if args.no_dag else ' gctree')] + cmds += ['micromamba install -y -c bioconda -c conda-forge phylip'] + cmds += ['micromamba install -y -c conda-forge%s click' % ('' if args.no_dag else ' gctree')] if args.no_dag: cmds += ['pip install gctree==3.3.0'] # I think having --user makes it install in ~/.local (outside mamba env) # micromamba remove -n gctree --all # to nuke it and start over diff --git a/projects/igphyml-run.py b/projects/igphyml-run.py index 3f1f4fde2..0b2909d1d 100755 --- a/projects/igphyml-run.py +++ b/projects/igphyml-run.py @@ -25,9 +25,9 @@ def install(): cmds = ['#!/bin/bash'] cmds += utils.mamba_cmds(args.env_label, only_prep=True) - cmds += ['micromamba create -n %s' % args.env_label] + cmds += ['micromamba create -y -n %s' % args.env_label] cmds += ['micromamba activate %s' % args.env_label] # python= 3.6 and 3.9 failed, so i let it choose, it chose 3.5 which seems to work - cmds += ['micromamba install -c bioconda -c conda-forge changeo'] + cmds += ['micromamba install -y -c bioconda -c conda-forge changeo'] # micromamba remove --all -n args.env_label # to nuke it and start over cmds += ['cd packages'] cmds += ['git clone https://bitbucket.org/kleinstein/igphyml']