Wiki¶

Tychus installation and pipeline testing¶

Installation¶

Clone the repository or specific branch by

git clone https://github.com/egeza/Tychus.git

git clone -b ilifu https://github.com/egeza/Tychus.git

Inside the Tychus dir fetch all (if you did clone the directory not just a branch) remote branches and check if they are all cloned

git fetch --all
git branch -a

We use ilifu cluster therefore we create a local branch for the ilifu remote branch

git checkout ilifu

Verify cloned branch is ilifu

git branch

Issues and how they were resolved¶

1. kSNP3 - kSNP3 repository doesn't exist anymore as a result, we resorted to getting the singularity images from Katie /cbio/projects/025/images/ , while debugging the pipeline.

2. Prokka image - Struggled with the tbl2asn (now called table2asn), first tried downloading the existing docker image from [[[https://github.com/tseemann/prokka#singularity]]] and [[[https://github.com/tseemann/prokka/issues/453]]] without success. We then used [[[https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/]]] as a referral from [[[https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/]]] to build a docker image on BST from a Dockerfile in /home/ephie/Tychus/dockerfiles/docker_prokka. Challenge of "no space left on device" was resolved by Gerrit by docker rmi docker_id -f and docker image prune -a -f . We then used the singularityware/docker2singularity to convert docker image to singularity and transferred it to ilifu /cbio/projects/025/images/prokka_latest.simg .
   On ilifu, edit the conf/ilifu_assembly.config file withName: AnnotateContigs{ container='/cbio/users/katie/singularity_containers/prokka.simg' to the correct prokka image. Remember to edit the CacheDir and container if using the images to run the pipeline in the same config file.

3. Alignment module of the pipeline
   When testing the pipeline with tutorial data, had issues when building indexes from the databases: ecoli plasmid and, its best to comment all external resources except the genome pointing to the reference of ecoli in tutorial

   genome = "$baseDir/tutorial/reference/EcoliK-12MG1655.fa"
   

   Also, accessing the JAVA from ilifu was an issue, thus, I commented on the line in conf/ilifu_alignment.config

   JAVA='/cbio/soft/jdk-11.0.2/bin'
   

   and removed the variable ${JAVA}/ when running trimmomatic in the alignment.nf file.

Reference genome of interest (/cbio/projects/025/Tychus_DBs) e.g.¶

Our reference is the Lactobacillus iners (https://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/Lactobacillus_iners/)