Can't pull Singularity image

[cedricusureau]

Hello,

When I run this command :

singularity pull --name nf-core-lncpipe.simg shub://nf-core/lncpipe

I got this:
FATAL: While pulling shub image: failed to get manifest for: shub://nf-core/lncpipe: the requested manifest was not found in singularity hub

Is there another way to pull the image ?

Thank you.

[apeltzer]

Please try: singularity pull docker://nfcore/lncpipe:dev - the pipeline hasn't been brought up to newest nf-core standards and still needs quite some polishing.

(Can't check atm, but that should work hopefully)

[cedricusureau]

Thank you. I tried with this image and former one, but I still have this issue when I run it :

Script compilation error
- file : /gpfs/scratch/cusureau/lncpipe/LncPipe_V2/lncpipe-master/LncRNAanalysisPipe.nf
- cause: Identifier `Run_fastQC` is already used by another definition @ line 849, column 17.
           process Run_fastQC {
                   ^

Script compilation error
- file : /gpfs/scratch/cusureau/lncpipe/LncPipe_V2/lncpipe-master/LncRNAanalysisPipe.nf
- cause: Identifier `Run_afterQC` is already used by another definition @ line 875, column 17.
           process Run_afterQC {
                   ^

Script compilation error
- file : /gpfs/scratch/cusureau/lncpipe/LncPipe_V2/lncpipe-master/LncRNAanalysisPipe.nf
- cause: Identifier `Run_FastP` is already used by another definition @ line 909, column 17.
           process Run_FastP {
                   ^

Script compilation error
- file : /gpfs/scratch/cusureau/lncpipe/LncPipe_V2/lncpipe-master/LncRNAanalysisPipe.nf
- cause: Identifier `Build_kallisto_index_of_GTF_for_quantification` is already used by another definition @ line 1443, column 17.
           process Build_kallisto_index_of_GTF_for_quantification {
                   ^

Script compilation error
- file : /gpfs/scratch/cusureau/lncpipe/LncPipe_V2/lncpipe-master/LncRNAanalysisPipe.nf
- cause: Identifier `Run_kallisto_for_quantification` is already used by another definition @ line 1460, column 17.
           process Run_kallisto_for_quantification {
                   ^

Script compilation error
- file : /gpfs/scratch/cusureau/lncpipe/LncPipe_V2/lncpipe-master/LncRNAanalysisPipe.nf
- cause: Identifier `Run_LncPipeReporter` is already used by another definition @ line 1582, column 17.
           process Run_LncPipeReporter {
                   ^

Script compilation error
- file : /gpfs/scratch/cusureau/lncpipe/LncPipe_V2/lncpipe-master/LncRNAanalysisPipe.nf
- cause: Identifier `Run_LncPipeReporter_without_Design` is already used by another definition @ line 1628, column 17.
           process Run_LncPipeReporter_without_Design {

Any idea ?

[apeltzer]

Yeah, @likelet has to make the pipeline stable ;-) Its not been worked on for quite a while unfortunately, not sure what the status is here - sorry to tell you that :-(

[likelet]

@apeltzer thanks for post reply to the issues.
@cedricusureau the nf-core-lncpipe is still under-development(I am working on polishing the updated code to meet the requirement of nf-core). For the message, this is because the version in master branch is supported by the old version of nextflow. I have fixed the code in the dev branch. In default, nf-core pull the master branch to the analysis, so the error occurs when you pull the singularity by nf-core running command.
If you still want to run LncPipe analysis, please move to https://github.com/likelet/LncPipe to use this version