nservant
Install ignores the provided python path
Hi,
In my config-install.txt, the path is given to a custom python 3.7.9 installation:
PREFIX = /home/apa/hic/hicpro/install BOWTIE2_PATH = /n/apps/CentOS7/install/bowtie2-2.4.2/bin/bowtie2 SAMTOOLS_PATH = /n/apps/CentOS7/install/samtools-1.9/bin/samtools R_PATH = /n/apps/CentOS7/install/r-4.0.0/bin/R PYTHON_PATH = /home/apa/hic/hiclib/python3/install/bin/python3.7
However, when running 'make configure', make completely ignores this path and defaults to the sitewide python path, which is totally nonsensical. I do not have root permissions there, and it has no business using that python build anyway:
make configure make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt prefix=/n/apps/CentOS7 make[1]: Entering directory '/home/apa/gcloud_stuff/hic/hicpro/HiC-Pro' ./scripts/install/install_dependencies.sh -c ./config-install.txt -p /home/apa/gcloud_stuff/hicpro/install -o /home/apa/gcloud_stuff/hicpro/install/HiC-Pro_3.0.0 -q Make sure internet connection works for your shell prompt under current user's privilege ... Starting HiC-Pro installation ... export /n/apps/CentOS7/install/bowtie2-2.4.2/bin/bowtie2 in PATH export /n/apps/CentOS7/install/samtools-1.9/bin/samtools in PATH export /n/apps/CentOS7/install/r-4.0.0/bin/R in PATH export /home/apa/gcloud_stuff/hic/hiclib/python3/install/bin/python3.7 in PATH Python v3.7.X or higher is needed [2.7.5 detected]. make[1]: *** [scripts/install/Makefile:41: configure] Error 1 make[1]: Leaving directory '/home/apa/gcloud_stuff/hic/hicpro/HiC-Pro' make: *** [Makefile:38: configure] Error 2
Please make the 'make' process respect the indicated python path in the config file.
Thanks, Ariel
Hi Could you please run ?
/home/apa/gcloud_stuff/hic/hiclib/python3/install/bin/python3.7 --version
I think it uses the right version, but I'm suspecting an issue when checking the version number .... Thanks
Hi,
That command returns "3.7.9".
The install process actually relies upon the sitewide 'python' command for its version checking, definitely not the config python path. I have verified this with a clean install on a google cloud VM. At my location the install dies because our sitewide 'python' is 2.7.5. On the cloud VM, the install dies because it is 2.7.12.
Only if I delete /usr/bin/python and replace it with a symlink to the config python path, does the install actually proceed.
Thanks, Ariel
arff, I know ! You need to put the path to the exec folder ...
BOWTIE2_PATH = /n/apps/CentOS7/install/bowtie2-2.4.2/bin/
SAMTOOLS_PATH = /n/apps/CentOS7/install/samtools-1.9/bin/
R_PATH = /n/apps/CentOS7/install/r-4.0.0/bin/
PYTHON_PATH = /home/apa/hic/hiclib/python3/install/bin/
Because, those paths are simply added to the PATH env variable.
Then, for instance, for python it runs ${PYTHON_PATH}/python
Sorry for the wait, I finally had a chance to re-attempt this off the cloud an in our sitewide environment, where I don't have root, and we use pyenv for python version control. The sitewide default is 2.7.5.
I have modified the config-install.txt as you indicated:
BOWTIE2_PATH = /n/apps/CentOS7/install/bowtie2-2.2.9/bin SAMTOOLS_PATH = /n/apps/CentOS7/install/samtools-1.2/bin R_PATH = /n/apps/CentOS7/install/r-3.6.1/bin PYTHON_PATH = /n/core/Bioinformatics/Software/HiC_Python_3.7.9/python3/bin
But the install still chooses the sitewide 2.7.5:
apa@cypress ~/arima/HiC-Pro$ make configure make -f ./scripts/install/Makefile CONFIG_SYS=./config-install.txt prefix=/n/apps/CentOS7 make[1]: Entering directory '/home/apa/arima/HiC-Pro' ./scripts/install/install_dependencies.sh -c ./config-install.txt -p /n/core/Bioinformatics/Software/HiC-Pro -o /n/core/Bioinformatics/Software/HiC-Pro/HiC-Pro_3.0.0 -q Make sure internet connection works for your shell prompt under current user's privilege ... Starting HiC-Pro installation ... export /n/apps/CentOS7/install/bowtie2-2.2.9/bin in PATH export /n/apps/CentOS7/install/samtools-1.2/bin in PATH export /n/apps/CentOS7/install/r-3.6.1/bin in PATH export /n/core/Bioinformatics/Software/HiC_Python_3.7.9/python3/bin in PATH Python v3.7.X or higher is needed [2.7.5 detected]. make[1]: *** [scripts/install/Makefile:41: configure] Error 1 make[1]: Leaving directory '/home/apa/arima/HiC-Pro' make: *** [Makefile:38: configure] Error 2
I have added the python 3.7.9 path to the front of $PATH manually, also re-aliased the 'python' command in my bashrc to the desired python3, I don't know how it is detecting sitewide still, but it is clearly ignoring the version in the config.txt...
Thanks, Ariel
