Bioconda gridss recipe doesn't contain gridsstools #448
Description
After trying to run gridss_extract_overlapping_fragments.sh through the container quay.io/biocontainers/gridss:2.10.2--0,
I found that the gridsstools binary wasn't present.
I was able to get a workaround by downloading the binary 'on the fly' and adding it to the PATH variable.
gridss_tools_path="$(mktemp -d)"
gridss_version="2.10.2"
wget -qO- "https://github.com/PapenfussLab/gridss/releases/download/v${gridss_version}/gridss-${gridss_version}.tar.gz" | \
tar xz -C "${gridss_tools_path}" --get "gridsstools"
# Add tmp path to path
export PATH="$PATH:$gridss_tools_path"
# Then run the extract fragments command
/usr/local/share/gridss-${gridss_version}-0/gridss_extract_overlapping_fragments.sh ...args
This then led me to the following error:
tmp.Y5OiAo/gridsstools: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
I updated the script to contain the LD_LIBRARY_PATH to include /usr/local/lib and I was able to continue.
Is there anyway to add this to the meta.yaml file for gridss?
Alexis.