SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
Hi, I'm new to shell and I have an issue with setting the pathway for SAMSA to location of samsa2 GitHub download, The location should be set with the lines:
IGNORE_DEPS=1 (which doesn't return any errors)
if [[ -d "${BASH_SOURCE%/}/../bash_scripts/lib/common.sh" ]]; then source "${BASH_SOURCE%/}/../bash_scripts/lib/common.sh"else ("bash package_installation.bash") source "../bash_scripts/lib/common.sh" fi
I entered these lines:
$ if [[ -d "${BASH_SOURCE%/}/C:/Users/maria/samsa2/bash_scripts/lib/common.sh" ]]; then source "${BASH_SOURCE%/}/C:/Users/maria/samsa2/bash_scripts/lib/common.sh" else source "C:/Users/maria/samsa2/bash_scripts/lib/common.sh" fi
Maria is username in this case.
However, when I enter the lines from the second point, shell 'freezes' and the command is not executed.
Any help would be much appreciated
Hi, I'm new to shell and I have an issue with setting the pathway for SAMSA to location of samsa2 GitHub download, The location should be set with the lines:
I entered these lines: $ if [[ -d "${BASH_SOURCE%/}/C:/Users/maria/samsa2/bash_scripts/lib/common.sh" ]]; then source "${BASH_SOURCE%/}/C:/Users/maria/samsa2/bash_scripts/lib/common.sh" else source "C:/Users/maria/samsa2/bash_scripts/lib/common.sh" fi
Maria is username in this case. However, when I enter the lines from the second point, shell 'freezes' and the command is not executed. Any help would be much appreciated