shunhuahan
commented
1 year ago Hi @dgodin19,
Thanks for reporting it. There are multiple variables that could cause this issue, including base conda environment and conda version. You could first try installing the exact version of perl-text-soundex and repeatmasker as follows, then try installing ngs_te_mapper2, see if it works. It's possible the repeatmasker version your conda was trying to install doesn't have a compatible version of perl-text-soundex in conda.
conda create --name ngs_te_mapper2_test
conda activate ngs_te_mapper2_test
conda install perl-text-soundex=3.05=pl526_1000
conda install repeatmasker=4.0.7=pl526_13
conda install ngs_te_mapper2- Here is a better alternative. To fully control the variables, I have exported the conda environment with a fresh install of ngs_te_mapper2. You could save this into a yaml file (such as
environment.yml), and install this test conda environment by doingmamba env create -f environment.ymlorconda env create -f environment.yml.name: ngs_te_mapper2_test2 channels: - conda-forge - bioconda - defaults dependencies: - _libgcc_mutex=0.1=conda_forge - _openmp_mutex=4.5=2_gnu - bcftools=1.16=hfe4b78e_1 - bedtools=2.30.0=h468198e_3 - biopython=1.79=py310h5764c6d_2 - bwa=0.7.17=h7132678_9 - bzip2=1.0.8=h7f98852_4 - c-ares=1.18.1=h7f98852_0 - ca-certificates=2022.9.24=ha878542_0 - curl=7.85.0=h7bff187_0 - entrez-direct=16.2=he881be0_1 - gettext=0.21.1=h27087fc_0 - gmp=6.1.2=hf484d3e_1000 - gnutls=3.5.19=h2a4e5f8_1 - gsl=2.7=he838d99_0 - hmmer=3.3.2=h87f3376_2 - htslib=1.16=h6bc39ce_0 - k8=0.2.5=hd03093a_2 - keyutils=1.6.1=h166bdaf_0 - krb5=1.19.3=h3790be6_0 - ld_impl_linux-64=2.39=hc81fddc_0 - libblas=3.9.0=16_linux64_openblas - libcblas=3.9.0=16_linux64_openblas - libcurl=7.85.0=h7bff187_0 - libdeflate=1.13=h166bdaf_0 - libedit=3.1.20191231=he28a2e2_2 - libev=4.33=h516909a_1 - libffi=3.4.2=h7f98852_5 - libgcc-ng=12.2.0=h65d4601_19 - libgfortran-ng=12.2.0=h69a702a_19 - libgfortran5=12.2.0=h337968e_19 - libgomp=12.2.0=h65d4601_19 - libidn2=2.3.4=h166bdaf_0 - liblapack=3.9.0=16_linux64_openblas - libnghttp2=1.47.0=hdcd2b5c_1 - libnsl=2.0.0=h7f98852_0 - libopenblas=0.3.21=pthreads_h78a6416_3 - libsqlite=3.39.4=h753d276_0 - libssh2=1.10.0=haa6b8db_3 - libstdcxx-ng=12.2.0=h46fd767_19 - libunistring=0.9.10=h7f98852_0 - libuuid=2.32.1=h7f98852_1000 - libzlib=1.2.13=h166bdaf_4 - minimap2=2.24=h7132678_1 - ncurses=6.3=h27087fc_1 - nettle=3.3=0 - ngs_te_mapper2=1.0.2=pyhdfd78af_1 - numpy=1.23.4=py310h53a5b5f_0 - openssl=1.1.1q=h166bdaf_1 - pcre=8.45=h9c3ff4c_0 - perl=5.26.2=h36c2ea0_1008 - perl-archive-tar=2.32=pl526_0 - perl-carp=1.38=pl526_3 - perl-common-sense=3.74=pl526_2 - perl-compress-raw-bzip2=2.087=pl526he1b5a44_0 - perl-compress-raw-zlib=2.087=pl526hc9558a2_0 - perl-exporter=5.72=pl526_1 - perl-exporter-tiny=1.002001=pl526_0 - perl-extutils-makemaker=7.36=pl526_1 - perl-io-compress=2.087=pl526he1b5a44_0 - perl-io-zlib=1.10=pl526_2 - perl-json=4.02=pl526_0 - perl-json-xs=2.34=pl526h6bb024c_3 - perl-list-moreutils=0.428=pl526_1 - perl-list-moreutils-xs=0.428=pl526_0 - perl-pathtools=3.75=pl526h14c3975_1 - perl-scalar-list-utils=1.52=pl526h516909a_0 - perl-text-soundex=3.05=pl526_1000 - perl-types-serialiser=1.0=pl526_2 - perl-xsloader=0.24=pl526_0 - pip=22.3=pyhd8ed1ab_0 - pysam=0.19.1=py310hff46b53_1 - python=3.10.6=h582c2e5_0_cpython - python_abi=3.10=2_cp310 - readline=8.1.2=h0f457ee_0 - repeatmasker=4.0.7=pl526_13 - rmblast=2.11.0=h6200dbe_0 - samtools=1.16.1=h6899075_1 - seqtk=1.3=h7132678_4 - setuptools=65.5.0=pyhd8ed1ab_0 - tk=8.6.12=h27826a3_0 - trf=4.09.1=hec16e2b_2 - tzdata=2022e=h191b570_0 - wget=1.20.3=ha56f1ee_1 - wheel=0.37.1=pyhd8ed1ab_0 - xz=5.2.6=h166bdaf_0 - zlib=1.2.13=h166bdaf_4
Let me know how these suggestions work out for you and I could potentially update ngs_te_mapper2 bioconda recipe or repo accordingly to prevent others from having the same issues as well. Thanks!
Best, Shunhua
cbergman
Hi,
I am trying to create the environment for ngs_te_mapper2. I have attempted to use either mamba or conda with:
mamba create -n ngs_te_mapper2 --channel bioconda ngs_te_mapper2
or conda create -n ngs_te_mapper2 --channel bioconda ngs_te_mapper2
and I run into:
Encountered problems while solving:
I tried downloading perl-text-soundex from conda forge, but I still run into the previous errors. Any ideas? I am using a linux subsystem on a windows machine.