funannotate-software
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— | funannotate-software [2021/08/05 08:03] – created aorth | ||
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+ | ====== funannotate ====== | ||
+ | funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). | ||
+ | ===== Information ===== | ||
+ | |||
+ | * Version: 1.8.7 | ||
+ | * Added: August, 2021 | ||
+ | * Link: https:// | ||
+ | |||
+ | ===== Usage ===== | ||
+ | |||
+ | See versions of funannotate that are available: | ||
+ | < | ||
+ | |||
+ | Load a particular version into your environment and run it: | ||
+ | |||
+ | < | ||
+ | $ funannotate --help</ | ||
+ | |||
+ | ===== Installation ====== | ||
+ | Notes from the sysadmin during installation: | ||
+ | |||
+ | < | ||
+ | $ rpm --rebuilddb --root=/ | ||
+ | $ wget https:// | ||
+ | $ sudo rpm --root=/ | ||
+ | $ sudo yum --installroot=/ | ||
+ | $ sudo cp / | ||
+ | $ sudo mount --bind /dev/ / | ||
+ | $ sudo mount -t proc procfs / | ||
+ | $ sudo mount -t sysfs sysfs / | ||
+ | $ sudo chroot / | ||
+ | # wget https:// | ||
+ | # bash Miniconda3-latest-Linux-x86_64.sh -b -p / | ||
+ | # eval " | ||
+ | # conda config --add channels defaults | ||
+ | # conda config --add channels bioconda | ||
+ | # conda config --add channels conda-forge | ||
+ | # conda install -n base mamba | ||
+ | # mamba create -p / | ||
+ | # env > before-conda | ||
+ | # conda activate / | ||
+ | # env > conda-funannotate-1.8.7 | ||
+ | # exit | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo chown aorth / | ||
+ | $ rsync -av / | ||
+ | $ sudo chown -R root:root / | ||
+ | $ sudo umount / | ||
+ | |||
+ | funannotate has over fifty dependencies and is essentially impossible to install without the use of [[https:// | ||
+ | |||
+ | To create the [[https:// | ||
+ | |||
+ | Install databases: | ||
+ | |||
+ | < | ||
+ | $ funannotate check --show-versions | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo chown aorth / | ||
+ | $ funannotate setup -d / | ||
+ | |||
+ | Run built-in tests: | ||
+ | |||
+ | < |
funannotate-software.txt · Last modified: 2023/04/20 21:21 by aorth