From ece9e0f28ea2634b5abbfd0b7cf0a6be5f1bf8db Mon Sep 17 00:00:00 2001 From: Katharina Hoff <39333668+KatharinaHoff@users.noreply.github.com> Date: Thu, 19 Dec 2024 10:46:34 +0100 Subject: [PATCH] Update README.md Addressing second part of https://github.com/Gaius-Augustus/BRAKER/issues/901 --- README.md | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 162eda3..a22ec6f 100644 --- a/README.md +++ b/README.md @@ -407,18 +407,12 @@ In order to set the environment variable for your current Bash session, type: Add the above lines to a startup script (e.g. `~/.bashrc`) in order to make it available to all bash sessions. -Perl scripts within GeneMark-ES/ET/EP/ETP are configured with default Perl location at `/usr/bin/perl`. - -If you are running GeneMark-ES/ET/EP/ETP in an Anaconda environment (or want to use Perl from the `$PATH` variable for any other reason), modify the shebang of all GeneMark-ES/ET/EP/ETP scripts with the following command located inside GeneMark-ES/ET/EP/ETP folder: - -``` -perl change_path_in_perl_scripts.pl "/usr/bin/env perl" -``` - You can check whether GeneMark-ES/ET/EP is installed properly by running the `check_install.bash` and/or executing examples in `GeneMark-E-tests` directory. GeneMark-ETP is downward compatible, i.e. it covers the functionality of GeneMark-EP and GeneMark-ET in BRAKER, too. +Warning: installing GeneMark-ETP for BRAKER in conda environments has lead to multiple problems reported by users (Issues!). We can not offer support for conda installations. Please use the singularity image instead. + #### AUGUSTUS Download AUGUSTUS from its master branch at . Unpack AUGUSTUS and install AUGUSTUS according to AUGUSTUS `README.TXT`. ***Do not use outdated AUGUSTUS versions from other sources, e.g. Debian package or Bioconda package! BRAKER highly depends in particular on an up-to-date Augustus/scripts directory, and other sources are often lagging behind.***