• allow TTS and RNATTS tags in addition to TIS and RNATIS.

• 3' end mapping
• centroid mapping
• 5' end mapping

• the genomeindexpath variable in the config file seems to be useless

"Distribution of aligned read lengths, to be sure they are mostly
between 26 and 34 nt, centred at 29-30 nt, and relatively even." - Sarah Svensson

• Rule that creates final report with our bash script

• currently gffread is used for the generation of a stable gtf/gff file for further processing
• gffread requires some post-processing
• it might be easier to combine everything into one script

• change default to "annotation.gff" / "genome.fa"
• ensure that retrieveAnnotation and retrieveGenome rules are used throughout the project

• add config parameter for Archea sites
• add config parameter for featurecounts ID

Check annotation files for minus coodinates, used for features spanning the origin, e.g:
pSYSG ena gene -1055 1914 . - . gene_id "BAD02057"; gene_name "sll8049"; gene_source "ena"; gene_biotype "protein_coding";

The associated stop codon had the coordinates -1055 -1052
ensembl #epicfail
ribotish crashes due to this

• for the same input, we get different output

Hi,

Thanks for your work on what seems to be an amazing tool! I can't wait to try it out once I figure out some small dependencies issues for which I could use some help.

I'm walking through the documentation that you provided ( https://hribo.readthedocs.io/en/latest/source/overview.html#tools ), and I am having some issues related to python dependencies.
It seemed that HRIBO relies on DeepRibo (both for DataParser.py and for DeepRibo.py), which I've cloned via git (from https://github.com/Biobix/DeepRibo ).

The issue that I'm having is that it seems DeepRibo relies on some deprecated type aliases (in particular np.int) from numpy. I've searched and these aliases seem to have been deprecated from numpy 1.20.

I breifly thought about updating these (for instance replacing np.int by np), but I was scared of going through the rabbit hole of having to fix more and more things on DeepRibo.

So I thought I'd use numpy in version 1.19.5, but then my python (which is setup from the environment.yaml provided) wasn't compatible with it. I tried to force (in the environment.yml) python to an older version (like 3.7) but I got even more dependencies issues during the execution of the command conda create --file HRIBO/environment.yaml

By the way, it seems the webpage https://hribo.readthedocs.io/en/latest/source/overview.html#tools recommends using python 3.7, but the environment.yaml provided explicitly requests python=3.11.0=he550d4f_1_cpython
Can I please ask which one are you using personally?

I'm wondering if you are still having a runnable version of HRIBO, if you could please export and publish an updated version of your working environment. That would be a great help to avoid the dependency issues.

Just a final question/remark about "conda create" versus "conda env create": the same webpage also recommends to use:
conda create --file HRIBO/environment.yaml
But that fails with the error: conda create: error: one of the arguments -n/--name -p/--prefix is required
So of course I've tried:
conda create --file HRIBO/environment.yaml -n hribo_env
But that fails with the error: CondaValueError: could not parse 'name: hribo_env' in: HRIBO/environment.yaml
I've searched a bit, and it seems (according to conda/conda#6827 but which is a fairly old thread) that "environment.yml doesn't work with conda install --file. You need to use conda env commands with environment.yml."
Therefore in everything I have attempted I have used:
conda env create --file HRIBO/environment.yaml
Is that what you would recommend to do as well?

Any help would be very much appreciated!
Kind regards.

• re/move temporary files from tracks folder
• make clear diagram of merging strategy (helps understanding of file names)
• update documentation (report) to better explain each file
• add potential names to tracks (check if predicted ORF already exists and add name)
• add colors for different tracks

• provide excel file

• delete all snakefiles that are obsolete
• we should have:

1. Snakefile
2. Snakefile_nixtail (rename)
3. Snakefile_paired_end
4. Snakefile_paired_end_nixtail ???
5. Snakefile_deepribo ??? (maybe combine this with Snakefile)

• maybe we should use temp() on files like genomeSegemehl index to remove them after they become obsolete

• a lot of useless folders are created
• many folders should be renamed

• remove flash and use segemehl for paired-end directly.
• requires changes in metagene profiling due to changes in bam files.

File 1: ORF information

• unique id
• start
• stop
• orf length
• potential RBS

• add a template for paired end data

• clean these files.
• remove old rules
• add new rules

Hi again,

In your config.yaml template under DE for contrasts the help is # comma-seperated list of condition contrasts: treated1_control1,treated2_control2...
but contrasts should be - separated and not _ (which is clear reading the docs however)

The --configfile HRIBO/config.yaml param for running the workflow is obsolete as the path is hardcoded in the Snakefile

Add configure fields to set start stop and SD track motifs and
also add them to the report

• add SortMeRNA as optional, atleast for the later galaxy version

• generate appropriate annotation (exon, cds, gtf format)
• update ribotish/all/tis to use the correct parameters

• würzburg is interested in gene synteny analysis

Hi Rick, the README states to clone [email protected]:gelhausr/HRIBO.git but the path is actually RickGelhausen/HRIBO.git