sunta3iouxos

has the support for cutandrun software ended?

1

There are still quite a few issues that need to be resolved or updated in my opinion.

ghostscript is not found

1

The given ghostscript "/home/user/mambaforge/envs/meme/bin/gs" is not an executable file. Warning: Cannot convert EPS file to PNG as no install of Image Magick or Ghostscript is usable.

the produced bam files do not have the canonical format: this is the one that has been produced: ``` samtools view -h /mnt/Z/Shared\ folder/Shared\ data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201074_S18_L000/A006200317_201074_S18_L000.bam | head -50 @HD VN:1.5...

if the provided path in the config file has a space the script will fail. The path in the scripts need to be "" (commented): "$fastq_directory"

This part rises after a successful meme analysis is perform and is due to some python scripts ```[info] Scaning the De Novo motifs for each peak Using motif +1 of...

While using source atactk.install.sh I got the following errors, but the script said that it correctly installed all packages, I am unsure how to test that it got what it...

Hi all, as with #270 I created a mamba/conda environment as follows: ```bash $mamba create -n rgts -c bioconda rgt $mamba activate rgts ``` the python version is 3.7.12: ```bash...

Hi all, I created a mamba/conda environment as follows: ```bash mamba create -n rgts -c bioconda rgt mamba activate rgts ``` the python version is 3.7.12: ```bash python Python 3.7.12...