Nothing provides perl-text-soundex error for ngs_te_mapper2

[dgodin19]

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:

• nothing provides perl-text-soundex needed by repeatmasker-4.0.7-pl5.22.0_1 #mamba or
  UnsatisfiableError: #conda

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.

[shunhuahan]

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 doing mamba env create -f environment.yml or conda 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 @dgodin19

Did you make any progress on getting ngs_te_mapper2 installed. If so, could you please let us know so we can close this issue?

Thanks,
Casey