CLIPper doesn't work with a different help document.

[IrisWEI-1996]

Hi I followed the instruction to install CLIPper in the clipper3 environment, but everytime when I want to use CLIPper or check for help documents, I would find this, which I think is something different, may I ask if anyone knows how to fix it?

[junjunlab]

i got a same situation ,have you figure it out ? i do not know how to do.

[algaebrown]

Hi @IrisWEI-1996 and @zhangjun-123
It seems that the command line tool CLIPper is calling peaksmodule.cc instead of call_main() in main.py.
It will be helpful if @zhangjun-123 can share with me the below info:

1. Your docker
2. Gcc version (I assume it’s the same as you showed me in email)
3. Conda info
4. Any output when running Python install setup.py or pip install .

It seems that you are able to install successfully on Ubuntu but not in WSL. Not sure why that is. But my WSL seems to work pretty okay...

Alternative installation way is by gnix (as shown in readme.md).

Thanks for your patience.

[gnilihzeux]

@algaebrown @IrisWEI-1996 @zhangjun-123 Did you solved this problem ?
Sorry to awaken this issue again, but I could not install clipper at all using several methods, including

• conda, v 4.8.5
• local install with root, CentOS release 6.9， python 2.7.14

By the way, my os is < centos7, so alternative method using docker is blocked.

[lynnhlee]

Hi @algaebrown,

Any new fixes or workarounds for this issue? I'm encountering it too: conda v 4.9.2, running on CentOS 7-8.2003 on institutional cluster, python 3.7.7

thanks,
-Lynn

[IrisWEI-1996]

Hi,
I've reinstalled the clipper and it works now. In case it can do for help, I would like to share the codes for instalment as below:

212 eval "$(/vol/biotools/F29/miniconda2/bin/conda shell.bash hook)"
213 unset PYTHONPATH
215 conda config --add channels defaults
216 conda config --add channels bioconda
217 conda config --add channels conda-forge
218 conda create -n clipper python=3.8 rsem samtools numpy Cython pandas
219 conda activate clipper
220 cd /vol/biotools/src/
222 git clone https://github.com/YeoLab/clipper.git
223 cd clipper
224 find . -mtime +13700 -exec touch {} \; -print
225 python setup.py install

[lynnhlee]

Hi,
I've reinstalled the clipper and it works now. In case it can do for help, I would like to share the codes for instalment as below:

212 eval "$(/vol/biotools/F29/miniconda2/bin/conda shell.bash hook)"
213 unset PYTHONPATH
215 conda config --add channels defaults
216 conda config --add channels bioconda
217 conda config --add channels conda-forge
218 conda create -n clipper python=3.8 rsem samtools numpy Cython pandas
219 conda activate clipper
220 cd /vol/biotools/src/
222 git clone https://github.com/YeoLab/clipper.git
223 cd clipper
224 find . -mtime +13700 -exec touch {} \; -print
225 python setup.py install

Thanks for the help. Unfortunately, still no luck...I get the same error/behavior

[algaebrown]

Hi Everyone,

sorry for the late reply. I wasn’t able to reproduce the error. However, I do find that old message comes from “peaksmodule.cc”. We are working to make the package available on PyPI and conda. Hopefully it will make installation less painful.
int usage(char *program_name) { fprintf(stderr,"Usage is %s [options] \n", program_name); fprintf(stderr,"file_in is a file with a list of the length of aligned reads (only the part that aligns) \n"); fprintf(stderr,"Options\n"); fprintf(stderr," -L <int> Effective Gene Length\n"); fprintf(stderr," -r <int> # of iterations \n"); fprintf(stderr," -f <int> input file containing read lengths \n"); fprintf(stderr," -a <float> B-H FDR cutoff, default(.05) ... gets very slow as alpha gets smaller\n"); fprintf(stderr," -T 1/0 default(0) print running time statistics \n"); fprintf(stderr,"Output:\n"); fprintf(stderr,"Significance Threshold [tab] Iterations with this observed threshold\n"); exit(8); return -1; }

[algaebrown]

@gnilihzeux current version of clipper should be on python 3

[marc-jones]

I was able to reproduce this bug within a Docker container created with:

FROM continuumio/miniconda3:4.8.2

# Install apt packages
RUN apt-get update \
    && apt-get install -y --no-install-recommends \
    procps=2:3.3.15-2 \
    g++=4:8.3.0-1 \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*

RUN git clone --depth 1 --branch 2.0.1 https://github.com/YeoLab/clipper.git

RUN conda env create -f /clipper/environment3.yml \
    && conda clean -a
ENV PATH /opt/conda/envs/clipper3/bin:$PATH

WORKDIR /clipper

RUN conda run -n clipper3 python setup.py install

Doing a bit more digging, the failure is during the import of clipper.src.peaks. While trying to debug what was going wrong, I added debug flags to the build process, and all of a sudden it worked! Adding the following line to the Dockerfile (above the final RUN command) results in the proper Clipper help documentation being shown:

ENV CFLAGS '-Wall -O0 -g'

This doesn't really address why the bug is happening though, but my experience of Cython includes is poor, and unfortunately I can't help any further. Hopefully having a reproducible environment will help with debugging though.

[marc-jones]

Removing the usage function from peaksmodule.cc and rebuilding results in a segmentation error when trying to run Clipper, so this might be linked to #88

[Oakento]

Hi @IrisWEI-1996 and @zhangjun-123 It seems that the command line tool CLIPper is calling peaksmodule.cc instead of call_main() in main.py. It will be helpful if @zhangjun-123 can share with me the below info:

1. Your docker
2. Gcc version (I assume it’s the same as you showed me in email)
3. Conda info
4. Any output when running Python install setup.py or pip install .

It seems that you are able to install successfully on Ubuntu but not in WSL. Not sure why that is. But my WSL seems to work pretty okay...

Alternative installation way is by gnix (as shown in readme.md).

Thanks for your patience.

Hi @algaebrown,

I also encounter the same issue. I am using debian 11 with gcc version 10.2.1 and conda version 4.10.3. The conda environment is created and clipper is built according to the installation guide in README file. Have you figured out how to fix it?