Resolve conflicts in conda with priority to conda-forge #282

TomKellyGenetics · 2020-10-02T14:18:28Z

See issue here: bioconda/bioconda-recipes#17186

leepc12 · 2020-10-06T22:16:39Z

Thanks for the contribution. Testing your PR on my end.
BTW did you get any errors while running pipeline's installer script?
I would like to keep prioritizing Conda's default channels like defaults and r over bioconda and conda-forge.

scripts/install_conda_env.sh

TomKellyGenetics · 2020-10-07T02:01:56Z

Thanks, the installer script works apart from the conda create step. I created a conda environment and installed the required packages individually to identify the issue (conda was taking a long time to solve the environment). I was able to run the pipeline once all required packages were installed (with conda 4.8.5 and python 3.8).

I've updated the PR to prioritise the default channel. The cause of the issue was outdated bioconda packages conflicting with conda-forge. I hope this will save others the time of installing the pipeline with current releases of dependencies.

leepc12 · 2020-10-21T18:24:51Z

I tested with your PR but failed with tons of conflicts. My Conda/Python version is 4.8.3/3.7.7.

TomKellyGenetics · 2020-10-23T00:42:49Z

Thanks for looking into it. Have you tried running the pipeline on Python 3.8? I've managed to get it to work by installing the dependencies separately and thought the bioconda / conda-forge conflict was causing the problem.

I can run the pipeline without errors in this environment. In case it helps to troubleshoot the issue for others, here are the details:

requirements.txt

# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
_libgcc_mutex=0.1=conda_forge
_openmp_mutex=4.5=1_gnu
_r-mutex=1.0.1=anacondar_1
aadict=0.2.3=pypi_0
aiohttp=3.6.2=py38h516909a_0
alabaster=0.7.12=pypi_0
alsa-lib=1.2.3=h516909a_0
appdirs=1.4.3=py_1
argcomplete=1.12.1=pyh9f0ad1d_0
asn1crypto=1.4.0=pyh9f0ad1d_0
asset=0.6.13=pypi_0
async-timeout=3.0.1=py_1000
attrs=20.2.0=pyh9f0ad1d_0
autouri=0.2.2=py_0
awscli=1.18.151=py38h32f6830_0
babel=2.8.0=pypi_0
bedtools=2.29.0=hc088bd4_3
binutils_impl_linux-64=2.35=h18a2f87_9
binutils_linux-64=2.35=heab0d09_28
bioconductor-biocgenerics=0.32.0=r36_0
bioconductor-biocparallel=1.20.0=r36he1b5a44_0
bioconductor-biostrings=2.54.0=r36h516909a_0
bioconductor-genomeinfodb=1.22.0=r36_0
bioconductor-genomeinfodbdata=1.2.2=r36_0
bioconductor-genomicranges=1.38.0=r36h516909a_0
bioconductor-iranges=2.20.0=r36h516909a_0
bioconductor-rhtslib=1.18.0=r36hdb70ac9_1
bioconductor-rsamtools=2.2.0=r36he1b5a44_0
bioconductor-s4vectors=0.24.0=r36h516909a_0
bioconductor-xvector=0.26.0=r36h516909a_0
bioconductor-zlibbioc=1.32.0=r36h516909a_0
boost=1.74.0=py38hd103949_0
boost-cpp=1.74.0=h9359b55_0
boto3=1.15.10=pyh9f0ad1d_0
botocore=1.18.10=pyh9f0ad1d_0
brotlipy=0.7.0=py38h1e0a361_1000
bwa=0.7.17=hed695b0_7
bwidget=1.9.14=0
bzip2=1.0.8=h516909a_3
c-ares=1.16.1=h516909a_3
ca-certificates=2020.6.20=hecda079_0
cachetools=4.1.1=py_0
cairo=1.16.0=h3fc0475_1005
caper=1.3.3=pypi_0
certifi=2020.6.20=py38h32f6830_0
cffi=1.14.3=py38h5bae8af_0
chardet=3.0.4=py38h32f6830_1007
colorama=0.4.3=py_0
coloredlogs=14.0=py38h32f6830_1
conda=4.8.5=py38h32f6830_1
conda-package-handling=1.7.0=py38h1e0a361_5
croo=0.5.2=pypi_0
cryptography=3.1.1=py38h766eaa4_0
curl=7.71.1=he644dc0_8
cutadapt=2.10=py38h0213d0e_1
cycler=0.10.0=py_2
dateparser=0.7.6=pyh9f0ad1d_0
deeptools=3.5.0=py_0
deeptoolsintervals=0.1.9=pypi_0
dill=0.3.2=pyh9f0ad1d_0
dnaio=0.4.2=py38h0213d0e_1
docker-py=4.3.1=py38h32f6830_0
docker-pycreds=0.4.0=py_0
docutils=0.15.2=py38_0
filelock=3.0.12=pyh9f0ad1d_0
fontconfig=2.13.1=h1056068_1002
freetype=2.10.2=he06d7ca_0
fribidi=1.0.10=h516909a_0
gawk=5.1.0=h516909a_0
gcc_impl_linux-64=7.5.0=hdb87b24_16
gcc_linux-64=7.5.0=hf34d7eb_28
gettext=0.19.8.1=hc5be6a0_1002
gfortran_impl_linux-64=7.5.0=h1104b78_16
gfortran_linux-64=7.5.0=ha781d05_28
giflib=5.2.1=h516909a_2
glib=2.66.1=h680cd38_0
globre=0.1.5=pypi_0
google-api-core=1.22.2=py38h32f6830_0
google-auth=1.22.0=py_0
google-cloud-core=1.4.1=pyh9f0ad1d_0
google-cloud-storage=1.31.2=pyh9f0ad1d_0
google-crc32c=1.0.0=py38h6d3b9ce_0
google-resumable-media=1.0.0=pyh9f0ad1d_0
googleapis-common-protos=1.52.0=py38h32f6830_0
graphite2=1.3.13=he1b5a44_1001
grpcio=1.31.0=py38h2c89da0_0
gsl=2.6=h294904e_0
gxx_impl_linux-64=7.5.0=h1104b78_16
gxx_linux-64=7.5.0=ha781d05_28
harfbuzz=2.7.2=hee91db6_0
htslib=1.9=h4da6232_3
humanfriendly=8.2=py38h32f6830_0
icu=67.1=he1b5a44_0
idna=2.10=pyh9f0ad1d_0
idr=2.0.4.2=py38hd504320_4
imagesize=1.2.0=pypi_0
importlib-metadata=2.0.0=py38h32f6830_0
importlib_metadata=2.0.0=0
iniconfig=1.0.1=pyh9f0ad1d_0
jmespath=0.10.0=pyh9f0ad1d_0
joblib=0.16.0=pypi_0
jpeg=9d=h516909a_0
kernel-headers_linux-64=2.6.32=h77966d4_13
kiwisolver=1.2.0=py38hbf85e49_0
krb5=1.17.1=hfafb76e_3
lark-parser=0.10.0=pypi_0
lcms2=2.11=hbd6801e_0
ld_impl_linux-64=2.35=h769bd43_9
libblas=3.8.0=17_openblas
libcblas=3.8.0=17_openblas
libcrc32c=1.1.1=he1b5a44_2
libcurl=7.71.1=hcdd3856_8
libdeflate=1.6=h516909a_0
libedit=3.1.20191231=h46ee950_2
libev=4.33=h516909a_1
libffi=3.2.1=he1b5a44_1007
libgcc=7.2.0=h69d50b8_2
libgcc-devel_linux-64=7.5.0=h42c25f5_16
libgcc-ng=9.3.0=h24d8f2e_16
libgfortran-ng=7.5.0=hdf63c60_16
libgomp=9.3.0=h24d8f2e_16
libiconv=1.16=h516909a_0
liblapack=3.8.0=17_openblas
libnghttp2=1.41.0=hab1572f_1
libopenblas=0.3.10=pthreads_hb3c22a3_4
libpng=1.6.37=hed695b0_2
libprotobuf=3.13.0=h8b12597_0
libssh2=1.9.0=hab1572f_5
libstdcxx-devel_linux-64=7.5.0=h4084dd6_16
libstdcxx-ng=9.3.0=hdf63c60_16
libtiff=4.1.0=hc7e4089_6
libuuid=2.32.1=h14c3975_1000
libwebp-base=1.1.0=h516909a_3
libxcb=1.13=h14c3975_1002
libxml2=2.9.10=h68273f3_2
lz4-c=1.9.2=he1b5a44_3
macs2=2.2.7.1=py38h0213d0e_1
make=4.3=h516909a_0
markupsafe=1.1.1=py38h1e0a361_1
matplotlib=3.3.2=0
matplotlib-base=3.3.2=py38h91b0d89_0
miniwdl=0.8.2=py_0
more-itertools=8.5.0=py_0
multidict=4.7.6=pypi_0
multiprocess=0.70.10=py38h1e0a361_0
mysql-connector-c=6.1.11=h876a3cc_1006
ncurses=6.2=he1b5a44_1
nomkl=1.0=h5ca1d4c_0
numpy=1.19.1=py38hbc27379_2
numpydoc=1.1.0=pypi_0
olefile=0.46=py_0
openblas=0.3.10=pthreads_hf183345_4
openjdk=11.0.8=hacce0ff_0
openssl=1.1.1h=h516909a_0
packaging=20.4=pyh9f0ad1d_0
pandas=1.1.2=py38h950e882_0
pango=1.42.4=h7062337_4
pcre=8.44=he1b5a44_0
pcre2=10.35=h2f06484_0
perl=5.30.3=h516909a_1
phantompeakqualtools=1.2.2=0
picard=2.20.7=0
pigz=2.3.4=hed695b0_1
pillow=7.2.0=py38h9776b28_1
pip=20.2.3=py_0
pixman=0.38.0=h516909a_1003
plotly=4.11.0=pyh9f0ad1d_0
pluggy=0.13.1=py38h32f6830_2
preseq=2.0.3=hc216eb9_5
protobuf=3.13.0=pypi_0
pthread-stubs=0.4=h14c3975_1001
py=1.9.0=pyh9f0ad1d_0
py2bit=0.3.0=pypi_0
pyasn1=0.4.8=py_0
pyasn1-modules=0.2.8=pypi_0
pybigwig=0.3.17=pypi_0
pycosat=0.6.3=py38h1e0a361_1004
pycparser=2.20=pyh9f0ad1d_2
pyfaidx=0.5.9.1=pyh864c0ab_1
pygments=2.7.1=pypi_0
pygtail=0.11.1=py_0
pyhocon=0.3.55=pypi_0
pyopenssl=19.1.0=py_1
pyparsing=2.4.7=pyh9f0ad1d_0
pysam=0.16.0.1=pypi_0
pysocks=1.7.1=py38h32f6830_1
pytest=6.1.0=py38h32f6830_0
python=3.8.5=h1103e12_9_cpython
python-dateutil=2.8.1=py_0
python-graphviz=0.14.1=pypi_0
python-json-logger=0.1.11=py_0
python_abi=3.8=1_cp38
pytz=2020.1=pyh9f0ad1d_0
pyyaml=5.3.1=pypi_0
r-base=3.6.3=he766273_3
r-bh=1.72.0_3=r36h6115d3f_1
r-bitops=1.0_6=r36hcdcec82_1004
r-catools=1.18.0=r36h0357c0b_1
r-core=3.0=r36h6115d3f_0
r-formatr=1.7=r36h6115d3f_2
r-futile.logger=1.4.3=r36h6115d3f_1003
r-futile.options=1.0.1=r36h6115d3f_1002
r-lambda.r=1.2.4=r36h6115d3f_1
r-rcpp=1.0.5=r36h0357c0b_0
r-rcurl=1.98_1.2=r36hcdcec82_1
r-snow=0.4_3=r36h6115d3f_1002
r-snowfall=1.84_6.1=r36h6115d3f_1003
r-spp=1.16.0=r36h0357c0b_1
readline=8.0=he28a2e2_2
regex=2020.9.27=py38h1e0a361_0
requests=2.24.0=pyh9f0ad1d_0
retrying=1.3.3=pypi_0
rsa=4.5=pypi_0
ruamel.yaml=0.16.12=py38h1e0a361_0
ruamel.yaml.clib=0.2.2=py38h1e0a361_0
ruamel_yaml=0.15.80=py38h1e0a361_1002
s3transfer=0.3.3=py38h32f6830_1
sambamba=0.6.6=2
samstats=0.2.1=py_0
samtools=1.7=1
scikit-learn=0.23.2=pypi_0
scipy=1.5.2=py38h8c5af15_0
sed=4.8=hbfbb72e_0
setuptools=49.6.0=py38h32f6830_1
six=1.15.0=pyh9f0ad1d_0
snowballstemmer=2.0.0=pypi_0
sphinx=3.2.1=pypi_0
sphinxcontrib-applehelp=1.0.2=pypi_0
sphinxcontrib-devhelp=1.0.2=pypi_0
sphinxcontrib-htmlhelp=1.0.3=pypi_0
sphinxcontrib-jsmath=1.0.1=pypi_0
sphinxcontrib-qthelp=1.0.3=pypi_0
sphinxcontrib-serializinghtml=1.1.4=pypi_0
sqlite=3.33.0=h4cf870e_0
sysroot_linux-64=2.12=h77966d4_13
tabix=0.2.6=ha92aebf_0
threadpoolctl=2.1.0=pypi_0
tk=8.6.10=hed695b0_0
tktable=2.10=h555a92e_3
toml=0.10.1=pyh9f0ad1d_0
tornado=6.0.4=py38h1e0a361_1
tqdm=4.50.0=pyh9f0ad1d_0
trimmomatic=0.39=1
tzlocal=2.1=pyh9f0ad1d_0
ucsc-bedclip=357=1
ucsc-bedgraphtobigwig=357=1
ucsc-bedtobigbed=357=1
ucsc-bigwigaverageoverbed=357=1
ucsc-bigwiginfo=357=1
ucsc-fetchchromsizes=357=h5eb252a_2
ucsc-twobittofa=357=1
ucsc-wigtobigwig=357=1
urllib3=1.25.10=py_0
wdltool=0.14=1
websocket-client=0.57.0=py38h32f6830_2
wheel=0.35.1=pyh9f0ad1d_0
xdg=4.0.1=py_1
xopen=0.8.4=pypi_0
xorg-fixesproto=5.0=h14c3975_1002
xorg-inputproto=2.3.2=h14c3975_1002
xorg-kbproto=1.0.7=h14c3975_1002
xorg-libice=1.0.10=h516909a_0
xorg-libsm=1.2.3=h84519dc_1000
xorg-libx11=1.6.12=h516909a_0
xorg-libxau=1.0.9=h14c3975_0
xorg-libxdmcp=1.1.3=h516909a_0
xorg-libxext=1.3.4=h516909a_0
xorg-libxfixes=5.0.3=h516909a_1004
xorg-libxi=1.7.10=h516909a_0
xorg-libxrender=0.9.10=h516909a_1002
xorg-libxtst=1.2.3=h516909a_1002
xorg-recordproto=1.14.2=h516909a_1002
xorg-renderproto=0.11.1=h14c3975_1002
xorg-xextproto=7.3.0=h14c3975_1002
xorg-xproto=7.0.31=h14c3975_1007
xz=5.2.5=h516909a_1
yaml=0.2.5=h516909a_0
yarl=1.6.0=pypi_0
zipp=3.2.0=py_0
zlib=1.2.11=h516909a_1009
zstd=1.4.5=h6597ccf_2

encode-atac-seq-pipeline.yml

name: encode-atac-seq-pipeline
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - _r-mutex=1.0.1=anacondar_1
  - aiohttp=3.6.2=py38h516909a_0
  - alsa-lib=1.2.3=h516909a_0
  - appdirs=1.4.3=py_1
  - argcomplete=1.12.1=pyh9f0ad1d_0
  - asn1crypto=1.4.0=pyh9f0ad1d_0
  - async-timeout=3.0.1=py_1000
  - attrs=20.2.0=pyh9f0ad1d_0
  - autouri=0.2.2=py_0
  - awscli=1.18.151=py38h32f6830_0
  - bedtools=2.29.0=hc088bd4_3
  - binutils_impl_linux-64=2.35=h18a2f87_9
  - binutils_linux-64=2.35=heab0d09_28
  - bioconductor-biocgenerics=0.32.0=r36_0
  - bioconductor-biocparallel=1.20.0=r36he1b5a44_0
  - bioconductor-biostrings=2.54.0=r36h516909a_0
  - bioconductor-genomeinfodb=1.22.0=r36_0
  - bioconductor-genomeinfodbdata=1.2.2=r36_0
  - bioconductor-genomicranges=1.38.0=r36h516909a_0
  - bioconductor-iranges=2.20.0=r36h516909a_0
  - bioconductor-rhtslib=1.18.0=r36hdb70ac9_1
  - bioconductor-rsamtools=2.2.0=r36he1b5a44_0
  - bioconductor-s4vectors=0.24.0=r36h516909a_0
  - bioconductor-xvector=0.26.0=r36h516909a_0
  - bioconductor-zlibbioc=1.32.0=r36h516909a_0
  - boost=1.74.0=py38hd103949_0
  - boost-cpp=1.74.0=h9359b55_0
  - boto3=1.15.10=pyh9f0ad1d_0
  - botocore=1.18.10=pyh9f0ad1d_0
  - brotlipy=0.7.0=py38h1e0a361_1000
  - bwa=0.7.17=hed695b0_7
  - bwidget=1.9.14=0
  - bzip2=1.0.8=h516909a_3
  - c-ares=1.16.1=h516909a_3
  - ca-certificates=2020.6.20=hecda079_0
  - cachetools=4.1.1=py_0
  - cairo=1.16.0=h3fc0475_1005
  - certifi=2020.6.20=py38h32f6830_0
  - cffi=1.14.3=py38h5bae8af_0
  - chardet=3.0.4=py38h32f6830_1007
  - colorama=0.4.3=py_0
  - coloredlogs=14.0=py38h32f6830_1
  - conda=4.8.5=py38h32f6830_1
  - conda-package-handling=1.7.0=py38h1e0a361_5
  - cryptography=3.1.1=py38h766eaa4_0
  - curl=7.71.1=he644dc0_8
  - cutadapt=2.10=py38h0213d0e_1
  - cycler=0.10.0=py_2
  - dateparser=0.7.6=pyh9f0ad1d_0
  - deeptools=3.5.0=py_0
  - dill=0.3.2=pyh9f0ad1d_0
  - dnaio=0.4.2=py38h0213d0e_1
  - docker-py=4.3.1=py38h32f6830_0
  - docker-pycreds=0.4.0=py_0
  - docutils=0.15.2=py38_0
  - filelock=3.0.12=pyh9f0ad1d_0
  - fontconfig=2.13.1=h1056068_1002
  - freetype=2.10.2=he06d7ca_0
  - fribidi=1.0.10=h516909a_0
  - gawk=5.1.0=h516909a_0
  - gcc_impl_linux-64=7.5.0=hdb87b24_16
  - gcc_linux-64=7.5.0=hf34d7eb_28
  - gettext=0.19.8.1=hc5be6a0_1002
  - gfortran_impl_linux-64=7.5.0=h1104b78_16
  - gfortran_linux-64=7.5.0=ha781d05_28
  - giflib=5.2.1=h516909a_2
  - glib=2.66.1=h680cd38_0
  - google-api-core=1.22.2=py38h32f6830_0
  - google-auth=1.22.0=py_0
  - google-cloud-core=1.4.1=pyh9f0ad1d_0
  - google-cloud-storage=1.31.2=pyh9f0ad1d_0
  - google-crc32c=1.0.0=py38h6d3b9ce_0
  - google-resumable-media=1.0.0=pyh9f0ad1d_0
  - googleapis-common-protos=1.52.0=py38h32f6830_0
  - graphite2=1.3.13=he1b5a44_1001
  - grpcio=1.31.0=py38h2c89da0_0
  - gsl=2.6=h294904e_0
  - gxx_impl_linux-64=7.5.0=h1104b78_16
  - gxx_linux-64=7.5.0=ha781d05_28
  - harfbuzz=2.7.2=hee91db6_0
  - htslib=1.9=h4da6232_3
  - humanfriendly=8.2=py38h32f6830_0
  - icu=67.1=he1b5a44_0
  - idna=2.10=pyh9f0ad1d_0
  - idr=2.0.4.2=py38hd504320_4
  - importlib-metadata=2.0.0=py38h32f6830_0
  - importlib_metadata=2.0.0=0
  - iniconfig=1.0.1=pyh9f0ad1d_0
  - jmespath=0.10.0=pyh9f0ad1d_0
  - jpeg=9d=h516909a_0
  - kernel-headers_linux-64=2.6.32=h77966d4_13
  - kiwisolver=1.2.0=py38hbf85e49_0
  - krb5=1.17.1=hfafb76e_3
  - lcms2=2.11=hbd6801e_0
  - ld_impl_linux-64=2.35=h769bd43_9
  - libblas=3.8.0=17_openblas
  - libcblas=3.8.0=17_openblas
  - libcrc32c=1.1.1=he1b5a44_2
  - libcurl=7.71.1=hcdd3856_8
  - libdeflate=1.6=h516909a_0
  - libedit=3.1.20191231=h46ee950_2
  - libev=4.33=h516909a_1
  - libffi=3.2.1=he1b5a44_1007
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-devel_linux-64=7.5.0=h42c25f5_16
  - libgcc-ng=9.3.0=h24d8f2e_16
  - libgfortran-ng=7.5.0=hdf63c60_16
  - libgomp=9.3.0=h24d8f2e_16
  - libiconv=1.16=h516909a_0
  - liblapack=3.8.0=17_openblas
  - libnghttp2=1.41.0=hab1572f_1
  - libopenblas=0.3.10=pthreads_hb3c22a3_4
  - libpng=1.6.37=hed695b0_2
  - libprotobuf=3.13.0=h8b12597_0
  - libssh2=1.9.0=hab1572f_5
  - libstdcxx-devel_linux-64=7.5.0=h4084dd6_16
  - libstdcxx-ng=9.3.0=hdf63c60_16
  - libtiff=4.1.0=hc7e4089_6
  - libuuid=2.32.1=h14c3975_1000
  - libwebp-base=1.1.0=h516909a_3
  - libxcb=1.13=h14c3975_1002
  - libxml2=2.9.10=h68273f3_2
  - lz4-c=1.9.2=he1b5a44_3
  - macs2=2.2.7.1=py38h0213d0e_1
  - make=4.3=h516909a_0
  - markupsafe=1.1.1=py38h1e0a361_1
  - matplotlib=3.3.2=0
  - matplotlib-base=3.3.2=py38h91b0d89_0
  - miniwdl=0.8.2=py_0
  - more-itertools=8.5.0=py_0
  - multiprocess=0.70.10=py38h1e0a361_0
  - mysql-connector-c=6.1.11=h876a3cc_1006
  - ncurses=6.2=he1b5a44_1
  - nomkl=1.0=h5ca1d4c_0
  - numpy=1.19.1=py38hbc27379_2
  - olefile=0.46=py_0
  - openblas=0.3.10=pthreads_hf183345_4
  - openjdk=11.0.8=hacce0ff_0
  - openssl=1.1.1h=h516909a_0
  - packaging=20.4=pyh9f0ad1d_0
  - pandas=1.1.2=py38h950e882_0
  - pango=1.42.4=h7062337_4
  - pcre=8.44=he1b5a44_0
  - pcre2=10.35=h2f06484_0
  - perl=5.30.3=h516909a_1
  - phantompeakqualtools=1.2.2=0
  - picard=2.20.7=0
  - pigz=2.3.4=hed695b0_1
  - pillow=7.2.0=py38h9776b28_1
  - pip=20.2.3=py_0
  - pixman=0.38.0=h516909a_1003
  - plotly=4.11.0=pyh9f0ad1d_0
  - pluggy=0.13.1=py38h32f6830_2
  - preseq=2.0.3=hc216eb9_5
  - pthread-stubs=0.4=h14c3975_1001
  - py=1.9.0=pyh9f0ad1d_0
  - pyasn1=0.4.8=py_0
  - pycosat=0.6.3=py38h1e0a361_1004
  - pycparser=2.20=pyh9f0ad1d_2
  - pyfaidx=0.5.9.1=pyh864c0ab_1
  - pygtail=0.11.1=py_0
  - pyopenssl=19.1.0=py_1
  - pyparsing=2.4.7=pyh9f0ad1d_0
  - pysocks=1.7.1=py38h32f6830_1
  - pytest=6.1.0=py38h32f6830_0
  - python=3.8.5=h1103e12_9_cpython
  - python-dateutil=2.8.1=py_0
  - python-json-logger=0.1.11=py_0
  - python_abi=3.8=1_cp38
  - pytz=2020.1=pyh9f0ad1d_0
  - r-base=3.6.3=he766273_3
  - r-bh=1.72.0_3=r36h6115d3f_1
  - r-bitops=1.0_6=r36hcdcec82_1004
  - r-catools=1.18.0=r36h0357c0b_1
  - r-core=3.0=r36h6115d3f_0
  - r-formatr=1.7=r36h6115d3f_2
  - r-futile.logger=1.4.3=r36h6115d3f_1003
  - r-futile.options=1.0.1=r36h6115d3f_1002
  - r-lambda.r=1.2.4=r36h6115d3f_1
  - r-rcpp=1.0.5=r36h0357c0b_0
  - r-rcurl=1.98_1.2=r36hcdcec82_1
  - r-snow=0.4_3=r36h6115d3f_1002
  - r-snowfall=1.84_6.1=r36h6115d3f_1003
  - r-spp=1.16.0=r36h0357c0b_1
  - readline=8.0=he28a2e2_2
  - regex=2020.9.27=py38h1e0a361_0
  - requests=2.24.0=pyh9f0ad1d_0
  - ruamel.yaml=0.16.12=py38h1e0a361_0
  - ruamel.yaml.clib=0.2.2=py38h1e0a361_0
  - ruamel_yaml=0.15.80=py38h1e0a361_1002
  - s3transfer=0.3.3=py38h32f6830_1
  - sambamba=0.6.6=2
  - samstats=0.2.1=py_0
  - samtools=1.7=1
  - scipy=1.5.2=py38h8c5af15_0
  - sed=4.8=hbfbb72e_0
  - setuptools=49.6.0=py38h32f6830_1
  - six=1.15.0=pyh9f0ad1d_0
  - sqlite=3.33.0=h4cf870e_0
  - sysroot_linux-64=2.12=h77966d4_13
  - tabix=0.2.6=ha92aebf_0
  - tk=8.6.10=hed695b0_0
  - tktable=2.10=h555a92e_3
  - toml=0.10.1=pyh9f0ad1d_0
  - tornado=6.0.4=py38h1e0a361_1
  - tqdm=4.50.0=pyh9f0ad1d_0
  - trimmomatic=0.39=1
  - tzlocal=2.1=pyh9f0ad1d_0
  - ucsc-bedclip=357=1
  - ucsc-bedgraphtobigwig=357=1
  - ucsc-bedtobigbed=357=1
  - ucsc-bigwigaverageoverbed=357=1
  - ucsc-bigwiginfo=357=1
  - ucsc-fetchchromsizes=357=h5eb252a_2
  - ucsc-twobittofa=357=1
  - ucsc-wigtobigwig=357=1
  - urllib3=1.25.10=py_0
  - wdltool=0.14=1
  - websocket-client=0.57.0=py38h32f6830_2
  - wheel=0.35.1=pyh9f0ad1d_0
  - xdg=4.0.1=py_1
  - xorg-fixesproto=5.0=h14c3975_1002
  - xorg-inputproto=2.3.2=h14c3975_1002
  - xorg-kbproto=1.0.7=h14c3975_1002
  - xorg-libice=1.0.10=h516909a_0
  - xorg-libsm=1.2.3=h84519dc_1000
  - xorg-libx11=1.6.12=h516909a_0
  - xorg-libxau=1.0.9=h14c3975_0
  - xorg-libxdmcp=1.1.3=h516909a_0
  - xorg-libxext=1.3.4=h516909a_0
  - xorg-libxfixes=5.0.3=h516909a_1004
  - xorg-libxi=1.7.10=h516909a_0
  - xorg-libxrender=0.9.10=h516909a_1002
  - xorg-libxtst=1.2.3=h516909a_1002
  - xorg-recordproto=1.14.2=h516909a_1002
  - xorg-renderproto=0.11.1=h14c3975_1002
  - xorg-xextproto=7.3.0=h14c3975_1002
  - xorg-xproto=7.0.31=h14c3975_1007
  - xz=5.2.5=h516909a_1
  - yaml=0.2.5=h516909a_0
  - zipp=3.2.0=py_0
  - zlib=1.2.11=h516909a_1009
  - zstd=1.4.5=h6597ccf_2
  - pip:
    - aadict==0.2.3
    - alabaster==0.7.12
    - asset==0.6.13
    - babel==2.8.0
    - caper==1.3.3
    - croo==0.5.2
    - deeptoolsintervals==0.1.9
    - globre==0.1.5
    - imagesize==1.2.0
    - joblib==0.16.0
    - lark-parser==0.10.0
    - multidict==4.7.6
    - numpydoc==1.1.0
    - protobuf==3.13.0
    - py2bit==0.3.0
    - pyasn1-modules==0.2.8
    - pybigwig==0.3.17
    - pygments==2.7.1
    - pyhocon==0.3.55
    - pysam==0.16.0.1
    - python-graphviz==0.14.1
    - pyyaml==5.3.1
    - retrying==1.3.3
    - rsa==4.5
    - scikit-learn==0.23.2
    - snowballstemmer==2.0.0
    - sphinx==3.2.1
    - sphinxcontrib-applehelp==1.0.2
    - sphinxcontrib-devhelp==1.0.2
    - sphinxcontrib-htmlhelp==1.0.3
    - sphinxcontrib-jsmath==1.0.1
    - sphinxcontrib-qthelp==1.0.3
    - sphinxcontrib-serializinghtml==1.1.4
    - threadpoolctl==2.1.0
    - xopen==0.8.4
    - yarl==1.6.0

Note some packages were installed by pip(3). This is a Linux Debian 9 server used for bioinformatics analyses so it's possible dependencies missing from conda were already installed on this system.

leepc12 · 2020-10-26T21:07:32Z

Base python3 (in base conda environment or your system's global python3) version doesn't matter. Running scripts/install_conda_env.sh will make a new Conda environment encode-atac-seq-pipeline and its python3 version will be fixed at 3.7 while resolving conflicts in dependencies. If you have 3.8 in there then something is wrong.

TomKellyGenetics · 2020-10-27T02:06:06Z

Thanks for explaining. If I understand correctly, the python version is fixed in scripts/requirements_py2.txt but not for python 3 scripts/requirements.txt. I've updated the requirements to behave as expected and avoid upgrading to newer python 3 versions.

If you don't think this is necessary, you may close the PR. I'm okay to simply leave it here in case it helps others running into same issue.

annashcherbina · 2021-06-11T18:40:43Z

Can we merge this in please? this seems to resolve all the install issues we have been having

TomKellyGenetics · 2021-06-12T06:58:51Z

For convenience, I've merged the latest version of the pipeline into my branch and resolved conflicts, i.e., applied the changes to both conda and mamba calls. 😄

leepc12 · 2021-06-24T21:33:46Z

Test this PR again but failed with lots of conflicts.
I added python == 3.7.9 to requirements.txt and modified the installer script like

...
  mamba create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y --strict-channel-priority --override-channels -c default -c r -c conda-forge -c bioconda
...
  conda create -n ${CONDA_ENV_PY3} --file ${REQ_TXT_PY3} -y --strict-channel-priority --override-channels -c default -c r -c conda-forge -c bioconda
...

Let me drop --strict-channel-priority and test again.

Resolve conflicts in conda with priority to conda-forge

2afad7a

See issue here: bioconda/bioconda-recipes#17186

TomKellyGenetics commented Oct 7, 2020

View reviewed changes

scripts/install_conda_env.sh Outdated Show resolved Hide resolved

Update scripts/install_conda_env.sh

d0c9c52

Set python 3 version to 3.7

740878d

TomKellyGenetics mentioned this pull request Nov 17, 2020

PyInquirer conda conflict for nf-core 1.10.2 and python 3.7 nf-core/tools#726

Closed

Merge branch 'master' into patch-1

658a076

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Resolve conflicts in conda with priority to conda-forge #282

Resolve conflicts in conda with priority to conda-forge #282

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Resolve conflicts in conda with priority to conda-forge #282

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