Comments (14)
Looks like I need to have a look at the conda package again...
from chipseq.
If anything like that does come up, then we should be able to do a workaround by mimicking those actions in the Dockerfile
and Singularity
file I figure.
from chipseq.
Hi @chuan-wang ,
I just merged in the required changes in bioconda, which should hopefully fix things without requiring that change (enforcing python2.7 to be used for the package there).
bioconda/bioconda-recipes#10406
This might take a while to be present in bioconda, then requiring us to rebuild the Docker Image and the Singularity Hub image, but should install fine after that. At least I was able to install properly after that :-)
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Package updated, I think the reason was simply the missing -y
parameter when installing the databases. Lets see if that helps. There also might exist some issues with Python, as this package requires strictly python2.7 to be present and uses python
in the respective script headers, so I might need to update that too - I will test this first and then fix the remaining issues on the go :-)
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Sounds good, thanks! 👍
I'm slightly paranoid that this could also be affected by our conda ENV
hack (no source activate
so no pre/post- hook activations). But hopefully it'll be fine..
from chipseq.
To be 100% sure, I also added the python <3.0a0
requirement to the file. It just feels safer and better in this context.
Yeah, I also had that feeling. Which could make things a bit more complicated in the installation unfortunately :-(
from chipseq.
Yup, I think that should be possible!
from chipseq.
Hello,
I found the following solution in case it is of any help:
In the ngsplotdb.py and setTableDefaults.py files change the first line from
#!/usr/bin/env python
to
#!/usr/bin/env python2
/chuan
from chipseq.
@apeltzer Good to know! Thanks for the work! XD
from chipseq.
Still need to do some fixes with bioconda. Slighly more complex as they blacklisted all R=3.4.1 packages right now and I had to get around this first of all.
Will keep you posted here and its high up my priority list...
from chipseq.
No hurry! We are still working on some bugs in the pipeline.
from chipseq.
Hi @apeltzer, just let you know that we are replacing the function of ngsplot with deepTools in PR #51. Hopefully you haven't spent too much time on fixing the ngsplot issue...Sorry that I should have told you earlier.
from chipseq.
Hi @chuan-wang , no worries - I'M skipping fixing that package now then and am more than happy to be able to do so...
from chipseq.
@apeltzer OK! XD
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Related Issues (20)
- No Space left on device error HOT 3
- Make subworkflows & modules available for nf-core tools HOT 1
- Default values for p-value and FDR HOT 2
- Get rid of checkIfExists for params paths HOT 1
- minor "samplesheet_pe.csv" format issue HOT 1
- PHANTOMPEAKQUALTOOLS throws stack overflow exception HOT 1
- MACS2: Too few paired peaks (0) so I can not build the model! HOT 2
- Error with NextSeq trimming HOT 2
- Error running the pipline test in the BWA index step HOT 2
- jobs failing with sigbus and unknown userid errors HOT 1
- Update MACS to v3 HOT 1
- There are multiple files for each of the following file names
- Can't run if there is no control HOT 2
- Improve website on parameters section Alignment Options for argument --save_unaligned HOT 1
- IDR analysis HOT 2
- Remove lib folder to get ready for v2.13.1 template merge HOT 1
- Macs2 Output HOT 2
- The "sample" field from the samplesheet is too lenient HOT 1
- Streamline nf-core/chipseq and nf-core/atacseq by using shared subworkflows
- Get rid of checksamplesheet.py and switch to nf-schema
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