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Oshlack / Slinker

Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.
MIT License
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Could not resolve specified command executor YOUR EXECUTOR as a valid file path or a class named any of bpipe.executor.YOUR EXECUTOR #7

Closed mariakondili closed 2 years ago

mariakondili commented 2 years ago

Hello, I have this issue for quiet a few days now, I cannot find out where the problem is ! Here is my script for running Slinker, after cloning the repo. I am launching in a cluster, after creating a private conda environment.

The environment created as follows :

Added following lines @ ~/.condarc

envs_dirs:
  - /shared/projects/<project_name>/conda/env
pkgs_dirs:
  - /shared/projects/<project_name>/conda/pkgs

And then ...

$ conda env create --file Slinker/env/slinker.yml

The script : 

#SBATCH --cpus-per-task 4 
module load java-jdk/11.0.9.1
export java=/soft/miniconda/envs/java-jdk-11.0.9.1/bin/java  #because I was getting error "java: not found"
export bpipe=/projects/Slinker/tools/bpipe-0.9.9.9/bin/bpipe
SLINKERDIR=/projects/Slinker
work_dir=/projects/run_slinker

bpipe -p case_sample=${SLINKERDIR}/tests/unhealthy_Aligned.sortedByCoord.out.bam \
 -p gene=ETV6 -p genome=19 -p a_mem=20000000000 -p g_mem=20000000000 \
 -p results=${work_dir}/test_results/  -p threads=4  ${SLINKERDIR}/workflows/slinker.groovy ${SLINKERDIR}/tests/*.bam

the slurm.out file reports: 

| Starting Pipeline at 2022-08-19 16:20  |

Stage make_dir (cases) 
ERROR: stage make_dir failed: Could not resolve specified command executor YOUR EXECUTOR as a valid file path or a class named any of bpipe.executor.YOUR EXECUTOR, bpipe.executor.YOUR EXECUTORCommandExecutor, YOUR EXECUTOR

= Pipeline Failed =

One or more parallel stages aborted. The following messages were reported:
--------------------------------------- make_dir  ( cases )  ---------------------------------------
Could not resolve specified command executor YOUR EXECUTOR as a valid file path or a class named any of bpipe.executor.YOUR EXECUTOR, bpipe.executor.YOUR EXECUTORCommandExecutor, YOUR EXECUTOR

----------------------------------------------------------------------------------------------------
Use 'bpipe errors' to see output from failed commands.

"bpipe errors" shows : 

======================== Found 0 failed commands from run []========================

..but before that, I would get same message with "Pipeline failed" and in "bpipe_errors" : java not found. So ,after I added the path of java executable I only have the "pipe failed" message and I cannot find where the command "YOUR EXECUTOR" refers to !
Concerning the make_dir, the test_results/ directory can be created, it is in my projects-path and i have rights to create.

breons commented 2 years ago

Hello!

So, that particular area in bpipe.config is referring to setting up Slinker (through bpipe) to work in your cluster environment: https://docs.bpipe.org/Guides/ResourceManagers/

If you're not running slinker on a cluster you should be able to just remove everything within "cluster configuration" in workflow/bpipe.config

Hopefully that gets you running!

mariakondili commented 2 years ago

Thanks ! I actually am running in cluster, so I added executor="slurm" & queue="fast" for my cluster's architecture, and it worked !