Lactobacillus iners MAGs: Genital inflammation in adolescent women

# Wiki

## Tychus installation and pipeline testing

### Installation

Clone the repository or specific branch by 

``` shell

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

``` shell

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 debugging

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.

1. 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" on the **BST machine** 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.

1. Alignment module of the pipeline

When testing the pipeline with *tutorial* data, we had issues when building indexes from the databases: ecoli virulence and plasmid, make sure that all lines under PATH TO EXTERNAL RESOURCES are commented out 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, so it's best to comment it out in *conf/ilifu_alignment.config* 

```

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

```

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

## Analysis of Lactobacillus iners

## 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/)