From 59e35329f42413ba8600f860c55a2e422673e93c Mon Sep 17 00:00:00 2001 From: Celio Santos-Jr Date: Mon, 30 Oct 2023 18:11:43 -0300 Subject: [PATCH] ENH Better information for installation (#66) * ENH fix pyrodigal version avoid error Newer versions of pyrodigal uses different command names for the old functions in the script, keeping the results. So, we fix the version to avoid breaking the code with different python versions. * ENH Include specification for dedicated environment Include instructions for installation of macrel inside a dedicated environment as the preferred method to work with Macrel. That is important to avoid conflict of common packages that most of the programs use in different versions that may conflict inside the Macrel's structure. * ENH installation instructions clarity make the recipe for installation using conda in a dedicated environment more clear. --- --- README.md | 8 ++++++++ install.sh | 2 +- 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f909d156..dfe78cf6 100644 --- a/README.md +++ b/README.md @@ -28,6 +28,14 @@ Macrel as a whole is under the **MIT** license. The recommended method of installation is through [bioconda](https://anaconda.org/bioconda/macrel): +```bash +conda create --name env_macrel -c bioconda macrel +conda activate env_macrel +macrel -h +``` + +Alternatively, just: + ```bash conda install -c bioconda macrel ``` diff --git a/install.sh b/install.sh index ad8b0a6e..f2b49cde 100755 --- a/install.sh +++ b/install.sh @@ -43,7 +43,7 @@ fi ${CONDA_INSTALL_CMD} install -y \ --prefix $BASEDIR/envs/Macrel_env \ ngless \ - "pyrodigal>=0.7.3" \ + "pyrodigal<3.0.0" \ megahit \ paladin \ pandas \