Commit af06e1e7 authored by josh's avatar josh
Browse files

Install numpy with pip to make metaphlan happy

also installing a few other python packages with pip to avoid pulling in numpy with apt-get
parent 1ded1a89
Pipeline #194207 passed with stages
in 168 minutes and 38 seconds
......@@ -176,7 +176,6 @@ RUN apt-get update && \
rna-star \
bwa \
trimmomatic \
python3-igraph \
abyss \
bc \
rdp-readseq \
......@@ -185,7 +184,7 @@ RUN apt-get update && \
librdp-taxonomy-tree-java \
clustalw \
fastqc
# sra-toolkit ipython \
# sra-toolkit ipython python3-igraph \
# RUN pip install qiime
......@@ -237,7 +236,9 @@ RUN mkdir -p $MANUAL_BIN $MANUAL_SHARE ; \
# DukeDSClient
RUN pip3 install --no-cache-dir DukeDSClient multiqc
# --------------------------------
# Install FastTree and FastTreeMP
# --------------------------------
RUN mkdir -p $MANUAL_BIN && \
wget --no-verbose -O $MANUAL_BIN/FastTree.c http://www.microbesonline.org/fasttree/FastTree-2.1.10.c && \
gcc -DUSE_DOUBLE -O3 -finline-functions -funroll-loops -Wall -o $MANUAL_BIN/FastTree $MANUAL_BIN/FastTree.c -lm && \
......@@ -245,19 +246,30 @@ RUN mkdir -p $MANUAL_BIN && \
chmod 555 $MANUAL_BIN/FastTree $MANUAL_BIN/FastTreeMP && \
rm $MANUAL_BIN/FastTree*.c
# -----------------
# Install Lefse
# -----------------
# R libraries: splines, stats4, survival, mvtnorm, modeltools, coin, MASS
RUN Rscript -e "install.packages(pkgs = c('coin'), \
repos=${CRAN_REPO}, \
dependencies=TRUE)"
# python libraries: rpy2 (v. 2.1 or higher), numpy, matplotlib (v. 1.0 or higher), argparse
RUN apt-get update && \
apt-get install -y --no-install-recommends \
python3-rpy2 \
python3-h5py \
nano \
jed
RUN pip3 install --no-cache-dir \
numpy \
matplotlib \
rpy2 \
h5py \
argparse
# RUN apt-get update && \
# apt-get install -y --no-install-recommends \
# python3-rpy2 \
# python3-h5py \
# nano \
# jed
RUN mkdir -p $MANUAL_BIN && \
cd $MANUAL_BIN && \
......
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