Question: Issue installing rmats using conda
gravatar for noahhelton98
5 weeks ago by
noahhelton980 wrote:

I am trying to install rmats using conda install -c bioconda rmats and I keep getting this issue

**UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:
  - rmats -> python[version='2.7.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0']
Your python: python=3.8
If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify

I have tried changing my python version to 3.7.0 by creating a virtual conda environment, but I got the same issue. Any suggestions?

rna-seq conda splicing rmats • 238 views
ADD COMMENTlink modified 5 weeks ago by benformatics2.0k • written 5 weeks ago by noahhelton980

If I read this correctly it needs python2.

ADD REPLYlink written 5 weeks ago by ATpoint41k

@ATpoint - Unfortunately the versions reported on the bioconda frontpages are unreliable (see also this issue). In fact, at the time of this writing the meta.yaml file of rmats doesn't impose any restriction on the python version.

ADD REPLYlink written 5 weeks ago by dariober11k

As of the newest release:

It is now:

Compatible with both Python 2 and Python 3

As a side note, I'm successfully running rmats v4.1.0 with python v3.6.5 installed through conda in August

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by benformatics2.0k

Do you run on Mac? I tried to do the build step and got this error:

rm: .so: No such file or directory rm: *.so.: No such file or directory cd rMATS_C; make; cd lbfgs_scipy && make gfortran -c -O2 -c -o lbfgsb.o lbfgsb.f gfortran -c -O2 -c -o linpack.o linpack.f gfortran -c -O2 -c -o timer.o timer.f

gfortran -c lbfgs_scipy/routines.f -o lbfgs_scipy/lbfgsb.o linpack.o blas.o timer.o gcc -I/Users/heltonn/opt/anaconda3/include -Wall -O2

-msse2 -funroll-loops -fopenmp -o rMATSexe src/main.c src/myfunc.c src/util.c src/cthreadpool.c lbfgs_scipy/lbfgsb.o lbfgs_scipy/linpack.o lbfgs_scipy/timer.o -L/Users/heltonn/opt/anaconda3/lib -lgsl -lgslcblas -lm -lgfortran -lgsl -lgslcblas -lgomp -lblas -llapack clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' clang: error: unsupported option '-fopenmp' make[1]: * [rMATSexe] Error 1 make: * [build] Error 2

and if I try to ./run_rmats I get this error:

Traceback (most recent call last): File "/Users/heltonn/rmats/rmats-turbo/", line 16, in <module> from rmatspipeline import run_pipe ModuleNotFoundError: No module named 'rmatspipeline'

Not quite sure of the issue.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by noahhelton980

Is this after installing it with conda or downloading the "pre-compiled" version?

ADD REPLYlink written 5 weeks ago by benformatics2.0k

I've tried both ways and get the same results.

ADD REPLYlink written 5 weeks ago by noahhelton980

Make a separate environment and install rmats in it. Avoiding these conflicts by making separate environments is the whole point of using conda.

ADD REPLYlink written 5 weeks ago by ashish570
gravatar for dariober
5 weeks ago by
WCIP | Glasgow | UK
dariober11k wrote:

Odd... I try to create a new environment with rmats and python 3.7 is what gets installed:

conda create -n tmp-rmats rmats
Collecting package metadata (current_repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.8.3
  latest version: 4.8.5

Please update conda by running

    $ conda update -n base conda

## Package Plan ##

  environment location: /home/dario/miniconda3/envs/tmp-rmats

  added / updated specs:
    - rmats

The following packages will be downloaded:

    package                    |            build
    ca-certificates-2020.6.20  |       hecda079_0         145 KB  conda-forge
    certifi-2020.6.20          |   py37he5f6b98_2         151 KB  conda-forge
    ld_impl_linux-64-2.35      |       h769bd43_9         617 KB  conda-forge
    libgcc-ng-9.3.0            |      h5dbcf3e_17         7.8 MB  conda-forge
    libgfortran-ng-7.5.0       |      hae1eefd_17          22 KB  conda-forge
    libgfortran4-7.5.0         |      hae1eefd_17         1.3 MB  conda-forge
    libgomp-9.3.0              |      h5dbcf3e_17         378 KB  conda-forge
    libopenblas-0.3.10         |pthreads_hb3c22a3_5         7.8 MB  conda-forge
    libstdcxx-ng-9.3.0         |      h2ae2ef3_17         4.0 MB  conda-forge
    ncurses-6.2                |       he1b5a44_2         991 KB  conda-forge
    numpy-1.19.2               |   py37h7ea13bd_1         5.2 MB  conda-forge
    pip-20.2.3                 |             py_0         1.1 MB  conda-forge
    python-3.7.8               |h6f2ec95_1_cpython        53.1 MB  conda-forge
    rmats-4.1.0                |   py37haa8df35_4         468 KB  bioconda
    setuptools-49.6.0          |   py37he5f6b98_2         944 KB  conda-forge
    sqlite-3.33.0              |       h4cf870e_1         1.4 MB  conda-forge
    star-2.7.6a                |                0         3.7 MB  bioconda
    tk-8.6.10                  |       hed695b0_1         3.2 MB  conda-forge
    zlib-1.2.11                |    h516909a_1010         106 KB  conda-forge
                                           Total:        92.2 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  ca-certificates    conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
  certifi            conda-forge/linux-64::certifi-2020.6.20-py37he5f6b98_2
  gsl                conda-forge/linux-64::gsl-2.6-h294904e_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35-h769bd43_9
  libblas            conda-forge/linux-64::libblas-3.8.0-17_openblas
  libcblas           conda-forge/linux-64::libcblas-3.8.0-17_openblas
  libffi             conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h5dbcf3e_17
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-7.5.0-hae1eefd_17
  libgfortran4       conda-forge/linux-64::libgfortran4-7.5.0-hae1eefd_17
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h5dbcf3e_17
  liblapack          conda-forge/linux-64::liblapack-3.8.0-17_openblas
  libopenblas        conda-forge/linux-64::libopenblas-0.3.10-pthreads_hb3c22a3_5
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h2ae2ef3_17
  ncurses            conda-forge/linux-64::ncurses-6.2-he1b5a44_2
  numpy              conda-forge/linux-64::numpy-1.19.2-py37h7ea13bd_1
  openssl            conda-forge/linux-64::openssl-1.1.1h-h516909a_0
  pip                conda-forge/noarch::pip-20.2.3-py_0
  python             conda-forge/linux-64::python-3.7.8-h6f2ec95_1_cpython
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  readline           conda-forge/linux-64::readline-8.0-he28a2e2_2
  rmats              bioconda/linux-64::rmats-4.1.0-py37haa8df35_4
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py37he5f6b98_2
  sqlite             conda-forge/linux-64::sqlite-3.33.0-h4cf870e_1
  star               bioconda/linux-64::star-2.7.6a-0
  tk                 conda-forge/linux-64::tk-8.6.10-hed695b0_1
  wheel              conda-forge/noarch::wheel-0.35.1-pyh9f0ad1d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010

Proceed ([y]/n)?
ADD COMMENTlink written 5 weeks ago by dariober11k

I have rmats installed in a separate environment and it uses python 3.7.

ADD REPLYlink written 5 weeks ago by ashish570
gravatar for benformatics
5 weeks ago by
ETH Zurich
benformatics2.0k wrote:

If your conda is not working specifically for rmats. You could try alternatively creating a Python 3.6 or Python 2.7 environment with conda and then downloading the pre-built package (for your respective python version) from the rmats maintainer:

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by benformatics2.0k

Is there any issues when trying to run rmats on Mac by chance? I have tried this a few different ways and I just can't seem to get it to work.

ADD REPLYlink written 5 weeks ago by noahhelton980
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