From a37219c185bc671d552379259f603b8393d9788d Mon Sep 17 00:00:00 2001 From: david Date: Fri, 27 Mar 2020 11:37:46 +0100 Subject: [PATCH] python-3.7.6: Add --prefix to pip If pip finds the system installation path not writable, it falls back to --user and installs into ~/.local. Of course, when this script runs, its system installation path should be writable. However, other errors in our environment, which prevent $PREFIX from being written to, might go undetected because of the fallback. Specify --prefix to abort if $PREFIX is not writable. --- python-3.7.6-0.build.sh | 92 ++++++++++++++++++++--------------------- 1 file changed, 46 insertions(+), 46 deletions(-) diff --git a/python-3.7.6-0.build.sh b/python-3.7.6-0.build.sh index e57e0c7..694f684 100755 --- a/python-3.7.6-0.build.sh +++ b/python-3.7.6-0.build.sh @@ -165,57 +165,57 @@ make install ) python3 -m ensurepip -pip3 install -I pip +pip3 install --prefix=$PREFIX -I pip -pip3 install ipython[all] +pip3 install --prefix=$PREFIX ipython[all] -pip3 install SciPy NumPy Matplotlib pandas SymPy nose statsmodels +pip3 install --prefix=$PREFIX SciPy NumPy Matplotlib pandas SymPy nose statsmodels # clean up some dirt that statsmodels placed also into $PREFIX rm -vf $PREFIX/LICENSE.txt rm -vf $PREFIX/setup.cfg -pip3 install Cython - -pip3 install pysam -pip3 install seaborn -pip3 install scikit-learn -# pip3 install metaseq # fails (Latest commit fa875d1 on Jan 10, 2017) -pip3 install Mako -pip3 install meson # required in mariux - -pip3 install cutadapt # Helpdesk 01/24/18 16:19, Sabrina Krakau -pip3 install pygobject # Helpdesk 03/26/18 14:19, Virginie Stanisla -pip3 install blink1 # Blink1-lib 07/04/18 12:00, Niclas Hofmann - -pip3 install umi-tools -pip3 install sphinx -pip3 install recommonmark -pip3 install fastcluster -pip3 install pydot -pip3 install pygraphviz -pip3 install deeptools -pip3 install HTSeq -pip3 install keras -pip3 install MotifScan # Alena 30.8.2018 -pip3 install MAmotif -pip3 install hic2cool # Helpdesk Robert Schoepflin 17.09.2018 -# pip3 install hifive # only python 2.7+ -pip3 install snakemake -pip3 install virtualenv # Donald -pip3 install odfpy # Donald -pip3 install Dumper # Thomas -pip3 install igraph -pip3 install louvain # monocle3 prep for Helene -pip3 install selenium # 19.7.19 Kreitler -> https://webxray.org/ -pip3 install cooltools # Maria Valieva 17.7.2019 -pip3 install gmpy # From viper context (Helpdesk Laura Glaser 9.8.2019) - -# pip3 install HiCExplorer # Would be a nice to have, but it likes to downgrade too much, pick some cherries -pip3 install HiCMatrix -pip3 install pyGenomeTracks - -pip3 install python-bioformats - -pip3 install jupyterlab # request Peter Arndt +pip3 install --prefix=$PREFIX Cython + +pip3 install --prefix=$PREFIX pysam +pip3 install --prefix=$PREFIX seaborn +pip3 install --prefix=$PREFIX scikit-learn +#pip3 install --prefix=$PREFIX metaseq # fails (Latest commit fa875d1 on Jan 10, 2017) +pip3 install --prefix=$PREFIX Mako +pip3 install --prefix=$PREFIX meson # required in mariux + +pip3 install --prefix=$PREFIX cutadapt # Helpdesk 01/24/18 16:19, Sabrina Krakau +pip3 install --prefix=$PREFIX pygobject # Helpdesk 03/26/18 14:19, Virginie Stanisla +pip3 install --prefix=$PREFIX blink1 # Blink1-lib 07/04/18 12:00, Niclas Hofmann + +pip3 install --prefix=$PREFIX umi-tools +pip3 install --prefix=$PREFIX sphinx +pip3 install --prefix=$PREFIX recommonmark +pip3 install --prefix=$PREFIX fastcluster +pip3 install --prefix=$PREFIX pydot +pip3 install --prefix=$PREFIX pygraphviz +pip3 install --prefix=$PREFIX deeptools +pip3 install --prefix=$PREFIX HTSeq +pip3 install --prefix=$PREFIX keras +pip3 install --prefix=$PREFIX MotifScan # Alena 30.8.2018 +pip3 install --prefix=$PREFIX MAmotif +pip3 install --prefix=$PREFIX hic2cool # Helpdesk Robert Schoepflin 17.09.2018 +#pip3 install --prefix=$PREFIX hifive # only python 2.7+ +pip3 install --prefix=$PREFIX snakemake +pip3 install --prefix=$PREFIX virtualenv # Donald +pip3 install --prefix=$PREFIX odfpy # Donald +pip3 install --prefix=$PREFIX Dumper # Thomas +pip3 install --prefix=$PREFIX igraph +pip3 install --prefix=$PREFIX louvain # monocle3 prep for Helene +pip3 install --prefix=$PREFIX selenium # 19.7.19 Kreitler -> https://webxray.org/ +pip3 install --prefix=$PREFIX cooltools # Maria Valieva 17.7.2019 +pip3 install --prefix=$PREFIX gmpy # From viper context (Helpdesk Laura Glaser 9.8.2019) + +# pip3 install --prefix=$PREFIX HiCExplorer # Would be a nice to have, but it likes to downgrade too much, pick some cherries +pip3 install --prefix=$PREFIX HiCMatrix +pip3 install --prefix=$PREFIX pyGenomeTracks + +pip3 install --prefix=$PREFIX python-bioformats + +pip3 install --prefix=$PREFIX jupyterlab # request Peter Arndt exit