python-lzo added to conda-forge: conda-forge/staged-recipes#3370

CGATOxford · Jul 28, 2017 · 4eb9e15 · 4eb9e15
1 parent 67e0e26
commit 4eb9e15
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/conda/environments/scripts-devel.yml b/conda/environments/scripts-devel.yml
@@ -12,7 +12,7 @@ dependencies:
 - gcc
 - zlib
 - libpng
-#- mysqlclient # I think this allows "import MySQLdb"
+- mysqlclient # for python -c "import MySQLdb"
 # bioinformatics tools
 - ucsc-wigtobigwig
 - ucsc-bedtobigbed
@@ -26,7 +26,7 @@ dependencies:
 - future
 - ggplot
 - jinja2
-- lzo
+- python-lzo
 - matplotlib
 - networkx
 - nose
@@ -48,7 +48,6 @@ dependencies:
 - pyyaml
 - pip:
   - bx-python==0.7.3
-#  - MySQL-python==1.2.5
 # R deps
 - r-base
 - r-coloc

diff --git a/install-CGAT-tools.sh b/install-CGAT-tools.sh
@@ -191,7 +191,7 @@ log "installing CGAT environment"
 # https://conda.io/docs/using/envs.html#use-environment-from-file
 
 if [[ $INSTALL_SCRIPTS ]] ; then
-   conda create -n ${CONDA_INSTALL_ENV} ${CONDA_INSTALL_TYPE} -y
+   conda create -q -n ${CONDA_INSTALL_ENV} cgat-scripts --override-channels -c bioconda -c conda-forge -c defaults -y
 else
    # to-update once we merge to master:
    # wget -O env.yml https://raw.githubusercontent.com/CGATOxford/cgat/conda/environments/${CONDA_INSTALL_TYPE}