accessing files in shared directories while software installed with conda

Hiya!

Is there a smart way of accessing the files in the bin directory of the soft installed via conda?

I am writing snakemake pipeline in which I rely on conda. In one of the rules, I need to run vardict followed by two scripts (namely teststrandbias.R and var2vcf.pl) which are to be found in the share/vardict-VERSION/. How can I reference those?

I'll be very grateful for advice!

conda vardict snakemake

• 1,314 views • link

written 6.4 years ago by kzkedzierska

dirname `which vardict` ?

• 0 views • link

updated 6.4 years ago by Ram

• written 6.4 years ago by Pierre Lindenbaum

0 answers

No answers yet.

More posts like this

Snakemake and conda directory structure
written 1.9 years ago by hpapoli

Hello, Snakemake suggests the following structure for the project directory: ![enter image description here][1] I have a few questions when using snakemake together with conda. …
How to use Anaconda/Miniconda more effectively ?
written 2.1 years ago by SomeOne •

Hello, I have installed miniconda on the workstation which i access over ssh. I have all my environments set up which I use over and …
Snakemake issue with wrappers
written 2.8 years ago by Begonia_pavonina •

I have issues when running a wrapper of BWA mem with Snakemake. The error message "No module named 'snakemake_wrapper_utils'" appear (see below). However, when checking …
VarDictJava - teststrandbias.R
written 3.1 years ago by accdg2022 •

Hi all, I am trying to optimise my use of **VarDictJava** for some **FFPE** sequenced samples with a **custom targeted panel**. So, I release the …
snakemake workflow to download GEOdatasets in r have error of missing output exception
written 3.6 years ago by firstorthopedicdoctor •

I am creating a snakemake workflow to download geodatasets. However, I get the following error ``` RuleException: CalledProcessError in file /home/sara/sara/Snakefile, line 8: Command 'set …
how to specify a specific conda environment in a specific rule with snakemake?
written 3.7 years ago by yangliu326459 •

Hi! I met a question about snakemake when I try to specify a conda env within a specific rule, but not influence other rules which …
Lockfile command not found
written 4.5 years ago by priya.bmg •

Hello I am trying to setup snakemake workflow to analyse long range sequencing reads in HPC. The script stops when it has lockfiles giving the …
Launch a snakefile involving multiple conda environment using an snakemake specific environment
written 6.1 years ago by regue.hadrien •

Hi everyone, I'm working on a snakefile involving several conda environements. As it's more simple (and avoid package troubles) to split each tools in a …
How to run pygraphviz on macOS in conda
written 7.0 years ago by michael.flower.14 •

I'm new to bioinformatics, and am trying to install pygraphviz, but have run into problems. I've tried searching for solutions, but can't work it out. …
Tutorial: Creating workflows with snakemake and conda
written 7.9 years ago by finswimmer

# Aim of this tutorial Do you know one of these situations? - During the installation of a new bioinformatic tool you have to solve …