software installation

[wcstcyx]

I have encountered the following problem.

Error: ERROR: placeholder '/root/miniconda3/envs/_build_placehold_placehold_placehold_placehold_placehold_p' too short in: glib-2.43.0-2

And then I followed your instruction: "If you see the following error, then update your Anaconda with conda update conda and downgrade it to 4.0.5 conda install conda==4.0.5." But it didn't work. I found that the problem came from

conda create -n aquas_chipseq --file requirements.txt -y -c defaults -c bioconda -c r

in your install_dependencies.sh. Then I read https://github.com/conda/conda-build/pull/877 and https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/fgDBJ2YwETI. My anaconda path is

/share_bio/nas5/amsszhangsh_group/wangcan/software/python/anaconda3

It seemed that when I run

conda create -n aquas_chipseq --file requirements.txt -y -c defaults -c bioconda -c r

the prefix was

/share_bio/nas5/amsszhangsh_group/wangcan/software/python/anaconda3/envs/aquas_chipseq

which consisted of 86 characters. Then I tried to limit it to 80 characters. So I trimmed the trailing 6 characters in aquas_chipseq and run

conda create -n aquas_c --file requirements.txt -y -c defaults -c bioconda -c r

And I succeeded. I found that conda 4.0.5 and 4.1.11 are no different on this problem. So the version of conda is not the point. To solve this problem without modifying your script, I re-installed the anaconda in a directory with a shorter absolute path

/share_bio/nas5/amsszhangsh_group/wangcan/anaconda3

Then there were no problem when I run install_dependencies.sh. If one does not want to re-install anaconda, I think to use conda create -p your_short_path can also work. For example, use

conda create -p /share_bio/nas5/amsszhangsh_group/wangcan/aquas_chipseq

to replace

conda create -n aquas_chipseq

in

conda create -n aquas_chipseq --file requirements.txt -y -c defaults -c bioconda -c r