Differences

This shows you the differences between two versions of the page.

--- funannotate-software [2021/08/05 08:03] – created aorth
+++ funannotate-software [2023/04/20 21:21] (current) – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Version: 1.8.7
+  * Version: 1.8.15
   * Added: August, 2021
+  * Updated: April, 2023
   * Link: https://github.com/nextgenusfs/funannotate
 ===== Usage =====
-See versions of funannotate that are available:
+Funannotate is installed in a dedicated "container" environment using [[https://docs.sylabs.io/guides/latest/user-guide/|Singularity]] (similar to Docker, but more suited to HPC environments) so you need to run it a bit differently than other software. Here is an example SLURM batch script, ''funannotate.sbatch'':
-<code>$ module avail funannotate</code>
-Load a particular version into your environment and run it:
+<code>#!/usr/bin/env bash
+#SBATCH -p batch
+#SBATCH -n 10
+#SBATCH -J funannotate
-<code>$ module load funannotate/1.8.7
+# Set up output directory in scratch
-$ funannotate --help</code>
+WORKDIR=/var/scratch/aorth/funannotate/2022-06-09
-===== Installation ======
+mkdir -p "$WORKDIR" && cd "$WORKDIR"
-Notes from the sysadmin during installation:
-<code>$ mkdir -p /var/tmp/chroot/funannotate
+echo "SLURM job ID $SLURM_JOBID using $WORKDIR on $SLURMD_NODENAME"
-$ rpm --rebuilddb --root=/var/tmp/chroot/funannotate
-$ wget https://hpc.ilri.cgiar.org/mirror/centos/7/os/x86_64/Packages/centos-release-7-9.2009.0.el7.centos.x86_64.rpm
-$ sudo rpm --root=/var/tmp/chroot/funannotate -i centos-release-7-9.2009.0.el7.centos.x86_64.rpm
-$ sudo yum --installroot=/var/tmp/chroot/funannotate install -y rpm-build yum gcc wget vim perl
-$ sudo cp /etc/resolv.conf /var/tmp/chroot/funannotate/etc
-$ sudo mount --bind /dev/ /var/tmp/chroot/funannotate/dev
-$ sudo mount -t proc procfs /var/tmp/chroot/funannotate/proc
-$ sudo mount -t sysfs sysfs /var/tmp/chroot/funannotate/sys
-$ sudo chroot /var/tmp/chroot/funannotate
-# wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-# bash Miniconda3-latest-Linux-x86_64.sh -b -p /export/apps/funannotate/conda
-# eval "$(/export/apps/funannotate/conda/bin/conda shell.bash hook)"
-# conda config --add channels defaults
-# conda config --add channels bioconda
-# conda config --add channels conda-forge
-# conda install -n base mamba
-# mamba create -p /export/apps/funannotate/1.8.7 funannotate
-# env > before-conda
-# conda activate /export/apps/funannotate/1.8.7
-# env > conda-funannotate-1.8.7
-# exit
-$ sudo mkdir -p /export/apps/funannotate/1.8.7
-$ sudo chown aorth /export/apps/funannotate/1.8.7
-$ rsync -av /var/tmp/chroot/funannotate/export/apps/funannotate/1.8.7/ /export/apps/funannotate/1.8.7
-$ sudo chown -R root:root /export/apps/funannotate/1.8.7
-$ sudo umount /var/tmp/chroot/funannotate/dev /var/tmp/chroot/funannotate/proc /var/tmp/chroot/funannotate/sys</code>
-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, I first installed funannotate/1.8.7 in a chroot on the local file system and then rsynced it over to the network applications directory. This is MUCH faster, but more importantly, it avoids random "permission denied" errors I was getting when installing on the network file system.
+DATADIR=/home/aorth/data
+rnaseq_ont="${DATADIR}/ayb_leaf_stem_root.fastq"
+genome="${DATADIR}/ayb_11chrs_assembly_soft_masked.fasta"
-To create the [[https://github.com/ilri/hpc-environment-modules/tree/master/funannotate|modulefile]] I compared the output ''env'' before and after loading the funannotate environment with Conda.
+# The most important thing is to bind the input files and output directory.
+singularity run \
+            --bind "$genome:$genome","$rnaseq_ont:$rnaseq_ont","$WORKDIR:$WORKDIR" \
+            /export/apps/funannotate/1.8.15/funannotate.sif \
+            funannotate train --input "$genome" \
+            --out "$WORKDIR" \
+            --nanopore_cdna "$rnaseq_ont" \
+            --max_intronlen 10000 \
+            --jaccard_clip --species "Sphenotylis stenocarpa" \
+            --cpus $SLURM_NTASKS</code>
-Install databases:
+Note the use of ''bind'' to map the input files and working directory from the compute node into the container.
+===== Installation ======
+Notes from the sysadmin during installation:
-<code>$ module load funannotate/1.8.7
+<code>$ export SINGULARITY_TMPDIR=/var/scratch/aorth
-$ funannotate check --show-versions
+$ mkdir $SINGULARITY_TMPDIR
-$ sudo mkdir -p /export/apps/funannotate/1.8.7/db
+$ singularity pull /var/scratch/funannotate.sif docker://nextgenusfs/funannotate:v1.8.15
-$ sudo chown aorth /export/apps/funannotate/1.8.7/db
+$ sudo mkdir -p /export/apps/funannotate/1.8.15
-$ funannotate setup -d /export/apps/funannotate/1.8.7/db</code>
+$ sudo cp /var/scratch/funannotate.sif /export/apps/funannotate/1.8.15</code>
 Run built-in tests:
-<code>$ funannotate test -t all --cpus 12</code>
+<code>singularity run \
+            /export/apps/funannotate/1.8.15/funannotate.sif \
+            funannotate test -t all --cpus 10</code>