Hello,
So after cloning the repository from rmats-turbo and installing all the dependencies , I am trying to run build_rmats --conda, but keep getting the following error:
build_rmats --conda
WARNING: A conda environment already exists at '/home/angelosk/rmats_turbo_dir/rmats-turbo/conda_envs/rmats' Remove existing environment (y/[n])? n
CondaSystemExit: Exiting.
CondaError: Run 'conda init' before 'conda activate'
Running with **y** to remove existing environment:
WARNING: A conda environment already exists at '/home/angelosk/rmats_turbo_dir/rmats-turbo/conda_envs/rmats' Remove existing environment (y/[n])? y
Channels:
defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done Package Plan environment location: /home/angelosk/rmats_turbo_dir/rmats-turbo/conda_envs/rmats
Proceed ([y]/n)? y
Preparing transaction: done Verifying transaction: done Executing transaction: done
To activate this environment, use
$ conda activate /home/angelosk/rmats_turbo_dir/rmats-turbo/conda_envs/rmats
To deactivate an active environment, use
$ conda deactivate
CondaError: Run 'conda init' before 'conda activate'
Tried the following solutions in different combinations which I found for said error as seen here, here and here, but I am not sure what i am missing here since from my understanding the environment should be created by build_rmats so these solutions do not exactly fit. Sorry if this happens to be lack of basic knowledge on my part.
The rmats_py36 is an environment where I installed specifically python 3.6.12 and Cython 0.29.21 before running build_rmats --conda
Solutions tried:
source ~/.bashrc
source activate base
conda init bash
conda init
conda activate /home/angelosk/rmats_turbo_dir/rmats-turbo/conda_envs/rmats
conda activate rmats_py36
As an extra step, I have tried to run the installation process without the --conda flag and it seems to be working, but again cannot run
test_rmats, prompting to the same error. The following messages are prompted after running build_rmats for the second time (PAIRADISE and DARTS have also been cloned):
make4: Leaving directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/bamtools/build' [ 85%]
Built target BamTools-utils make4: Entering directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/bamtools/build' make4:
Leaving directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/bamtools/build' make4:
Entering directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/bamtools/build' [ 86%]
Linking CXX executable ../../../bin/bamtools make4: Leaving
directory '/home/angelosk/rmats_turbo_dir/rmats-turbo/bamtools/build'
[100%] Built target bamtools_cmd make3: Leaving directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/bamtools/build' make2:
Leaving directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/bamtools/build' rm -f to
ignore nonexistent files since *.dylib will only exist for mac cd
bamtools/lib; rm -f *.so .so. .dylib cd rMATS_C; make; make2:
Entering directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/rMATS_C' cd lbfgs_scipy &&
make make3: Entering directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/rMATS_C/lbfgs_scipy'
/usr/bin/gfortran -c -O2 -c -o lbfgsb.o lbfgsb.f /usr/bin/gfortran -c
-O2 -c -o linpack.o linpack.f /usr/bin/gfortran -c -O2 -c -o timer.o timer.f make3: Leaving directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/rMATS_C/lbfgs_scipy'
/usr/bin/gcc -I/usr/include -Wall -O2 -msse2 -funroll-loops -fopenmp
-o rMATSexe src/main.c src/myfunc.c src/util.c lbfgs_scipy/lbfgsb.o lbfgs_scipy/linpack.o lbfgs_scipy/timer.o -L/usr/lib/x86_64-linux-gnu
-lgsl -lgslcblas -lm -lm -lgfortran -lgsl -lgslcblas -lgomp -lblas -llapack make clean make3: Entering directory '/home/angelosk/rmats_turbo_dir/rmats- turbo/rMATS_C' rm -rf util.o
myfunc.o .o src/.o lbfgs_scipy/.o make3: Leaving directory
'/home/angelosk/rmats_turbo_dir/rmats-turbo/rMATS_C' make2: Leaving
directory '/home/angelosk/rmats_turbo_dir/rmats-turbo/rMATS_C' cd
rMATS_pipeline; python setup.py build_ext; running build_ext cp find
./rMATS_pipeline/build | grep so .; Loading required package:
doParallel Loading required package: foreach Loading required package:
iterators Loading required package: parallel Loading required package:
nloptr Loading required package: PAIRADISE Loading required package:
doSNOW Loading required package: foreach Loading required package:
iterators Loading required package: snow Loading required package:
getopt Loading required package: ggplot2 Loading required package:
mixtools mixtools package, version 2.0.0, Released 2022-12-04 This
package is based upon work supported by the National Science
Foundation under Grant No. SES-0518772 and the Chan Zuckerberg Initiative: Essential Open Source Software for Science (Grant No. 2020-255193).
Loading required package: Rcpp Loading required package: Darts
Thank you in advance for any assistance.
