simone-pignotti

Support for optimization of RNA structure

3

Even though the `AvoidHairpins` specification is a good compromise between speed and quality of the results, there are few tools available for optimizing RNA structure accurately (none actually usable programmatically,...

Transfer annotations from similar genome

5

Hi, thanks for developing this great tool! I believe a great addition to the workflow would be the possibility to provide a pre-annotated genome as input, allowing to: 1. speed...

Host removal parameter - pre-built bowtie2 index

2

### Description of feature Hi, In the host removal module, the bowtie index needs to be recomputed from `--host_fasta` for each execution. Would it be possible to add `--host_bt2` or...

No bases were counted for orf

1

Hello, I occasionally run into this issue when running PhySpy: ``` 2022-03-28 12:14:53 INFO Welcome to PhiSpy.py version 4.2.21 2022-03-28 12:14:53 INFO Starting PhiSpy.py with the following arguments Namespace(infile='input/genomic.gbff', output_dir='/home/ec2-user/physpy',...

Hi, is there a way to set parameters like `server_dir` and `load_server_directory` when running the docker image? I am not familiar with the Shiny framework, and it's not clear to...

Hello, I have added a very simple `Dockerfile` and `docker-compose.yml` based on the [official node.js documentation](https://nodejs.org/en/docs/guides/nodejs-docker-webapp/). - The `Dockerfile` defines the building process (`node:14` base image + `npm install`) and...