Troobleshooting with bioconda install
El-Castor opened this issue · 3 comments
El-Castor commented
Hi,
I have try to use your WGBS pipeline but when I launch the conda environment install following this command:
conda install -c bioconda trim-galore bismark bowtie2 samtools fastq-screen picard multiqcI have many error :
conda install -c bioconda trim-galore bismark bowtie2 samtools fastq-screen picard multiqc
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.7.12
latest version: 4.8.3
Please update conda by running
$ conda update -n base conda
## Package Plan ##
environment location: /opt/share/FLOCAD/userspace/cpichot/miniconda3/envs/CpG_me
added / updated specs:
- bismark
- bowtie2
- fastq-screen
- multiqc
- picard
- samtools
- trim-galore
The following packages will be downloaded:
package | build
---------------------------|-----------------
bowtie-1.2.3 | py36hdb11119_1 989 KB bioconda
bowtie2-2.4.1 | py36h7f0b59b_2 12.7 MB bioconda
brotlipy-0.7.0 |py36h8c4c3a4_1000 346 KB conda-forge
bz2file-0.98 | py_0 9 KB conda-forge
cffi-1.14.0 | py36hd463f26_0 221 KB conda-forge
chardet-3.0.4 |py36h9f0ad1d_1006 188 KB conda-forge
cryptography-2.9.2 | py36h45558ae_0 613 KB conda-forge
cutadapt-1.18 | py36h14c3975_1 206 KB bioconda
fastq-screen-0.14.0 | pl526_0 1.8 MB bioconda
hisat2-2.2.0 | py36h831f99a_3 13.3 MB bioconda
idna-2.9 | py_1 52 KB conda-forge
krb5-1.17.1 | hfafb76e_1 1.5 MB conda-forge
libgd-2.2.5 | h307a58e_1007 302 KB conda-forge
perl-gd-2.71 | pl526he860b03_0 114 KB bioconda
perl-gdgraph-1.54 | pl526_0 61 KB bioconda
perl-gdtextutil-0.86 | pl526h14c3975_5 21 KB bioconda
pigz-2.3.4 | hed695b0_1 76 KB conda-forge
pycparser-2.20 | py_0 89 KB conda-forge
pyopenssl-19.1.0 | py_1 47 KB conda-forge
pysocks-1.7.1 | py36h9f0ad1d_1 27 KB conda-forge
python-3.6.10 |h8356626_1011_cpython 34.1 MB conda-forge
requests-2.24.0 | pyh9f0ad1d_0 47 KB conda-forge
trim-galore-0.6.5 | 0 40 KB bioconda
urllib3-1.25.9 | py_0 92 KB conda-forge
xopen-0.7.3 | py_0 11 KB bioconda
------------------------------------------------------------
Total: 66.8 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_llvm
_r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1
alsa-lib conda-forge/linux-64::alsa-lib-1.1.5-h516909a_1002
binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.34-h53a641e_5
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.34-hc952b39_20
bismark bioconda/noarch::bismark-0.22.3-0
bowtie bioconda/linux-64::bowtie-1.2.3-py36hdb11119_1
bowtie2 bioconda/linux-64::bowtie2-2.4.1-py36h7f0b59b_2
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py36h8c4c3a4_1000
bwidget conda-forge/linux-64::bwidget-1.9.14-0
bz2file conda-forge/noarch::bz2file-0.98-py_0
bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_2
ca-certificates conda-forge/linux-64::ca-certificates-2020.6.20-hecda079_0
cairo conda-forge/linux-64::cairo-1.16.0-hcf35c78_1003
certifi conda-forge/linux-64::certifi-2020.6.20-py36h9f0ad1d_0
cffi conda-forge/linux-64::cffi-1.14.0-py36hd463f26_0
chardet conda-forge/linux-64::chardet-3.0.4-py36h9f0ad1d_1006
click conda-forge/noarch::click-7.1.2-pyh9f0ad1d_0
coloredlogs conda-forge/linux-64::coloredlogs-14.0-py36h9f0ad1d_1
colormath conda-forge/noarch::colormath-3.0.0-py_2
cryptography conda-forge/linux-64::cryptography-2.9.2-py36h45558ae_0
curl conda-forge/linux-64::curl-7.69.1-h33f0ec9_0
cutadapt bioconda/linux-64::cutadapt-1.18-py36h14c3975_1
cycler conda-forge/noarch::cycler-0.10.0-py_2
decorator conda-forge/noarch::decorator-4.4.2-py_0
expat conda-forge/linux-64::expat-2.2.9-he1b5a44_2
fastq-screen bioconda/noarch::fastq-screen-0.14.0-pl526_0
fastqc bioconda/noarch::fastqc-0.11.9-0
font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0
fontconfig conda-forge/linux-64::fontconfig-2.13.1-h86ecdb6_1001
freetype conda-forge/linux-64::freetype-2.10.2-he06d7ca_0
fribidi conda-forge/linux-64::fribidi-1.0.9-h516909a_0
future conda-forge/linux-64::future-0.18.2-py36h9f0ad1d_1
gcc_impl_linux-64 conda-forge/linux-64::gcc_impl_linux-64-7.5.0-hd420e75_6
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-7.5.0-h09487f9_20
gettext conda-forge/linux-64::gettext-0.19.8.1-hc5be6a0_1002
gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-7.5.0-hdf63c60_6
gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-7.5.0-h09487f9_20
giflib conda-forge/linux-64::giflib-5.2.1-h516909a_2
glib conda-forge/linux-64::glib-2.65.0-h6f030ca_0
graphite2 conda-forge/linux-64::graphite2-1.3.13-he1b5a44_1001
gsl conda-forge/linux-64::gsl-2.6-h294904e_0
gxx_impl_linux-64 conda-forge/linux-64::gxx_impl_linux-64-7.5.0-hdf63c60_6
gxx_linux-64 conda-forge/linux-64::gxx_linux-64-7.5.0-h09487f9_20
harfbuzz conda-forge/linux-64::harfbuzz-2.4.0-h9f30f68_3
hisat2 bioconda/linux-64::hisat2-2.2.0-py36h831f99a_3
htslib bioconda/linux-64::htslib-1.9-h4da6232_3
humanfriendly conda-forge/linux-64::humanfriendly-8.2-py36h9f0ad1d_0
icu conda-forge/linux-64::icu-64.2-he1b5a44_1
idna conda-forge/noarch::idna-2.9-py_1
importlib-metadata conda-forge/linux-64::importlib-metadata-1.6.1-py36h9f0ad1d_0
jinja2 conda-forge/noarch::jinja2-2.11.2-pyh9f0ad1d_0
jpeg conda-forge/linux-64::jpeg-9d-h516909a_0
kiwisolver conda-forge/linux-64::kiwisolver-1.2.0-py36hdb11119_0
krb5 conda-forge/linux-64::krb5-1.17.1-hfafb76e_1
lcms2 conda-forge/linux-64::lcms2-2.11-hbd6801e_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.34-h53a641e_5
libblas conda-forge/linux-64::libblas-3.8.0-16_openblas
libcblas conda-forge/linux-64::libcblas-3.8.0-16_openblas
libcurl conda-forge/linux-64::libcurl-7.69.1-hf7181ac_0
libdeflate bioconda/linux-64::libdeflate-1.2-h516909a_1
libedit conda-forge/linux-64::libedit-3.1.20191231-h46ee950_0
libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007
libgcc-ng conda-forge/linux-64::libgcc-ng-9.2.0-h24d8f2e_2
libgd conda-forge/linux-64::libgd-2.2.5-h307a58e_1007
libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-hdf63c60_6
libgomp conda-forge/linux-64::libgomp-9.2.0-h24d8f2e_2
libiconv conda-forge/linux-64::libiconv-1.15-h516909a_1006
liblapack conda-forge/linux-64::liblapack-3.8.0-16_openblas
libopenblas conda-forge/linux-64::libopenblas-0.3.9-h5ec1e0e_0
libpng conda-forge/linux-64::libpng-1.6.37-hed695b0_1
libssh2 conda-forge/linux-64::libssh2-1.9.0-hab1572f_2
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-9.2.0-hdf63c60_2
libtiff conda-forge/linux-64::libtiff-4.1.0-hc3755c2_3
libuuid conda-forge/linux-64::libuuid-2.32.1-h14c3975_1000
libwebp conda-forge/linux-64::libwebp-1.0.2-h56121f0_5
libxcb conda-forge/linux-64::libxcb-1.13-h14c3975_1002
libxml2 conda-forge/linux-64::libxml2-2.9.10-hee79883_0
llvm-openmp conda-forge/linux-64::llvm-openmp-10.0.0-hc9558a2_0
lz4-c conda-forge/linux-64::lz4-c-1.9.2-he1b5a44_1
lzstring conda-forge/noarch::lzstring-1.0.4-py_1001
make conda-forge/linux-64::make-4.3-h516909a_0
markdown conda-forge/noarch::markdown-3.2.2-py_0
markupsafe conda-forge/linux-64::markupsafe-1.1.1-py36h8c4c3a4_1
matplotlib-base conda-forge/linux-64::matplotlib-base-3.2.2-py36hb8e4980_0
multiqc bioconda/noarch::multiqc-1.9-pyh9f0ad1d_0
ncurses conda-forge/linux-64::ncurses-6.1-hf484d3e_1002
networkx conda-forge/noarch::networkx-2.4-py_1
numpy conda-forge/linux-64::numpy-1.18.5-py36h7314795_0
openjdk conda-forge/linux-64::openjdk-11.0.1-h600c080_1018
openssl conda-forge/linux-64::openssl-1.1.1g-h516909a_0
pango conda-forge/linux-64::pango-1.42.4-h7062337_4
pcre conda-forge/linux-64::pcre-8.44-he1b5a44_0
pcre2 conda-forge/linux-64::pcre2-10.35-h2f06484_0
perl conda-forge/linux-64::perl-5.26.2-h516909a_1006
perl-gd bioconda/linux-64::perl-gd-2.71-pl526he860b03_0
perl-gdgraph bioconda/linux-64::perl-gdgraph-1.54-pl526_0
perl-gdtextutil bioconda/linux-64::perl-gdtextutil-0.86-pl526h14c3975_5
picard bioconda/noarch::picard-2.23.0-0
pigz conda-forge/linux-64::pigz-2.3.4-hed695b0_1
pip conda-forge/noarch::pip-20.1.1-py_1
pixman conda-forge/linux-64::pixman-0.38.0-h516909a_1003
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h14c3975_1001
pycparser conda-forge/noarch::pycparser-2.20-py_0
pyopenssl conda-forge/noarch::pyopenssl-19.1.0-py_1
pyparsing conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
pysocks conda-forge/linux-64::pysocks-1.7.1-py36h9f0ad1d_1
python conda-forge/linux-64::python-3.6.10-h8356626_1011_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.8.1-py_0
python_abi conda-forge/linux-64::python_abi-3.6-1_cp36m
pyyaml conda-forge/linux-64::pyyaml-5.3.1-py36h8c4c3a4_0
r-base conda-forge/linux-64::r-base-4.0.1-h95c6c4b_0
readline conda-forge/linux-64::readline-8.0-hf8c457e_0
requests conda-forge/noarch::requests-2.24.0-pyh9f0ad1d_0
samtools bioconda/linux-64::samtools-1.9-h10a08f8_12
sed conda-forge/linux-64::sed-4.7-h1bed415_1000
setuptools conda-forge/linux-64::setuptools-47.3.1-py36h9f0ad1d_0
simplejson bioconda/linux-64::simplejson-3.8.1-py36_0
six conda-forge/noarch::six-1.15.0-pyh9f0ad1d_0
spectra conda-forge/noarch::spectra-0.0.11-py_1
sqlite conda-forge/linux-64::sqlite-3.30.1-hcee41ef_0
tbb conda-forge/linux-64::tbb-2020.1-hc9558a2_0
tk conda-forge/linux-64::tk-8.6.10-hed695b0_0
tktable conda-forge/linux-64::tktable-2.10-h555a92e_3
tornado conda-forge/linux-64::tornado-6.0.4-py36h8c4c3a4_1
trim-galore bioconda/noarch::trim-galore-0.6.5-0
urllib3 conda-forge/noarch::urllib3-1.25.9-py_0
wheel conda-forge/noarch::wheel-0.34.2-py_1
xopen bioconda/noarch::xopen-0.7.3-py_0
xorg-fixesproto conda-forge/linux-64::xorg-fixesproto-5.0-h14c3975_1002
xorg-inputproto conda-forge/linux-64::xorg-inputproto-2.3.2-h14c3975_1002
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h14c3975_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h516909a_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-h84519dc_1000
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.6.9-h516909a_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h14c3975_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h516909a_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h516909a_0
xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-5.0.3-h516909a_1004
xorg-libxi conda-forge/linux-64::xorg-libxi-1.7.10-h516909a_0
xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.10-h516909a_1002
xorg-libxtst conda-forge/linux-64::xorg-libxtst-1.2.3-h516909a_1002
xorg-recordproto conda-forge/linux-64::xorg-recordproto-1.14.2-h516909a_1002
xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h14c3975_1002
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h14c3975_1002
xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h14c3975_1007
xz conda-forge/linux-64::xz-5.2.5-h516909a_0
yaml conda-forge/linux-64::yaml-0.2.5-h516909a_0
zipp conda-forge/noarch::zipp-3.1.0-py_0
zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1006
zstd conda-forge/linux-64::zstd-1.4.4-h6597ccf_3
Proceed ([y]/n)? y
Downloading and Extracting Packages
cryptography-2.9.2 | 613 KB | ############################################################################# | 100%
perl-gd-2.71 | 114 KB | ############################################################################# | 100%
pyopenssl-19.1.0 | 47 KB | ############################################################################# | 100%
chardet-3.0.4 | 188 KB | ############################################################################# | 100%
pysocks-1.7.1 | 27 KB | ############################################################################# | 100%
bowtie-1.2.3 | 989 KB | ############################################################################# | 100%
pigz-2.3.4 | 76 KB | ############################################################################# | 100%
bz2file-0.98 | 9 KB | ############################################################################# | 100%
xopen-0.7.3 | 11 KB | ############################################################################# | 100%
hisat2-2.2.0 | 13.3 MB | ############################################################################# | 100%
fastq-screen-0.14.0 | 1.8 MB | ############################################################################# | 100%
requests-2.24.0 | 47 KB | ############################################################################# | 100%
trim-galore-0.6.5 | 40 KB | ############################################################################# | 100%
cutadapt-1.18 | 206 KB | ############################################################################# | 100%
idna-2.9 | 52 KB | ############################################################################# | 100%
pycparser-2.20 | 89 KB | ############################################################################# | 100%
bowtie2-2.4.1 | 12.7 MB | ############################################################################# | 100%
perl-gdtextutil-0.86 | 21 KB | ############################################################################# | 100%
krb5-1.17.1 | 1.5 MB | ############################################################################# | 100%
perl-gdgraph-1.54 | 61 KB | ############################################################################# | 100%
python-3.6.10 | 34.1 MB | ############################################################################# | 100%
cffi-1.14.0 | 221 KB | ############################################################################# | 100%
urllib3-1.25.9 | 92 KB | ############################################################################# | 100%
libgd-2.2.5 | 302 KB | ############################################################################# | 100%
brotlipy-0.7.0 | 346 KB | ############################################################################# | 100%
Preparing transaction: done
Verifying transaction: \
SafetyError: The package for r-base located at /opt/share/FLOCAD/userspace/cpichot/miniconda3/pkgs/r-base-4.0.1-h95c6c4b_0
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
reported size: 2946 bytes
actual size: 17754 bytes
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/convert_quals.pl'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/gen_2b_occ_lookup.pl'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/gen_occ_lookup.pl'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/gen_solqual_lookup.pl'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/infer_fraglen.pl'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_a_thaliana_tair.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_b_taurus_UMD3.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_c_elegans.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_canFam2.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_d_melanogaster.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_e_coli.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_h_sapiens_ncbi36.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_h_sapiens_ncbi37.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_hg18.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_hg19.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_m_musculus_ncbi37.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_mm9.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_rn4.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/make_s_cerevisiae.sh'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/test/DNA.pm'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/test/big_data/reads/human_reads.fa'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/test/big_data/reads/mouse_reads.fa'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/test/btdata.py'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/test/dataface.py'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/test/large_idx.py'
ClobberError: This transaction has incompatible packages due to a shared path.
packages: bioconda::bowtie-1.2.3-py36hdb11119_1, bioconda::bowtie2-2.4.1-py36h7f0b59b_2
path: 'bin/scripts/test/simple_tests.pl'
done
Executing transaction: doneAre the bioconda package available ?Do you have any suggestion please ?
Thanks in advance
ben-laufer commented
Hi @El-Castor, thanks for getting in touch about this. I think it's worth updating your conda to the newer version, but it looks to me like the error is from Bowtie1 and Bowtie2 clashing, since I believe Bowtie1 is included in Bismark by default. Can you try removing Bowtie2 from the command then just installing it on its own through conda after? Please let me know how that goes.
El-Castor commented
Hi @ben-laufer,
Whithout bowtie2 it work well, is it already implemented in bismark.
Thank for your fast response and your help.
regards
ben-laufer commented
It does look like Bowtie2 is now a dependency for Bismark in conda, so you should be good to go. Thanks for pointing this out, I'll update the documentation.