funannotate-software
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funannotate-software [2021/08/05 08:03] – created aorth | funannotate-software [2023/04/20 21:21] (current) – aorth | ||
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===== Information ===== | ===== Information ===== | ||
- | * Version: 1.8.7 | + | * Version: 1.8.15 |
* Added: August, 2021 | * Added: August, 2021 | ||
+ | * Updated: April, 2023 | ||
* Link: https:// | * Link: https:// | ||
===== Usage ===== | ===== Usage ===== | ||
- | See versions of funannotate that are available: | + | Funannotate is installed in a dedicated " |
- | < | + | |
- | Load a particular version into your environment and run it: | + | < |
+ | #SBATCH -p batch | ||
+ | #SBATCH -n 10 | ||
+ | #SBATCH -J funannotate | ||
- | < | + | # Set up output directory in scratch |
- | $ funannotate --help</ | + | WORKDIR=/ |
- | ===== Installation ====== | + | mkdir -p " |
- | Notes from the sysadmin during installation: | + | |
- | < | + | echo "SLURM job ID $SLURM_JOBID using $WORKDIR on $SLURMD_NODENAME" |
- | $ 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://conda.io/miniconda.html|Miniconda]]. My strategy is to install Conda somewhere globally and then use it to install funannotate. After the installation is done I think we don't technically need Conda itself anymore, as all binaries seem to be linked against libraries in the funannotate/1.8.7 directory. Furthermore, | + | DATADIR=/home/aorth/data |
+ | rnaseq_ont=" | ||
+ | genome=" | ||
- | To create | + | # The most important thing is to bind the input files and output directory. |
+ | singularity run \ | ||
+ | | ||
+ | | ||
+ | funannotate train --input " | ||
+ | --out " | ||
+ | --nanopore_cdna " | ||
+ | --max_intronlen 10000 \ | ||
+ | --jaccard_clip --species " | ||
+ | --cpus $SLURM_NTASKS</ | ||
- | Install databases: | + | Note the use of '' |
+ | |||
+ | ===== Installation ====== | ||
+ | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ funannotate check --show-versions | + | $ mkdir $SINGULARITY_TMPDIR |
- | $ sudo mkdir -p / | + | $ singularity pull / |
- | $ sudo chown aorth /export/apps/ | + | $ sudo mkdir -p / |
- | $ funannotate setup -d / | + | $ sudo cp /var/scratch/ |
Run built-in tests: | Run built-in tests: | ||
- | < | + | < |
+ | / | ||
+ | |
funannotate-software.1628150596.txt.gz · Last modified: 2021/08/05 08:03 by aorth