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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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Specific RMBlast version needed? #71

Closed oushujun closed 4 years ago

oushujun commented 4 years ago

Hello,

I tried to configure RepeatModeler 2.0.1 using conda installed packages. Others seem to work but the RMBlast path is always dropped by the configure script although it indicated "configured" when giving it the path at the beginning.

I tried the rmblast installed through the conda RepeatMasker 4.0.9_p2, and the standalone rmblast from conda, and the older versions (v2.2.28 and v2.6.0) of rmblast installed in our server, all indicated succeed by the configure script but then dropped (shown un-configured when trying to re-configure).

From the readme there is a precompiled rmblast from here, it's currently the 2.10.0 version, and it was also not recognized/dropped by the configure script.

After the "successful" message from configure, if I execute RepeatModeler there is an exit error:

./RepeatModeler Can't locate WUBlastSearchEngine.pm in @INC (you may need to install the WUBlastSearchEngine module) (@INC contains: /home/oushujun/las/bin/miniconda2/envs/EDTA/bin /work/LAS/mhufford-lab/oushujun/bin/RepeatModeler /work/LAS/mhufford-lab/oushujun/bin/miniconda2/envs/EDTA/lib/site_perl/5.26.2/x86_64-linux-thread-multi /work/LAS/mhufford-lab/oushujun/bin/miniconda2/envs/EDTA/lib/site_perl/5.26.2 /work/LAS/mhufford-lab/oushujun/bin/miniconda2/envs/EDTA/lib/5.26.2/x86_64-linux-thread-multi /work/LAS/mhufford-lab/oushujun/bin/miniconda2/envs/EDTA/lib/5.26.2 .) at /work/LAS/mhufford-lab/oushujun/bin/RepeatModeler/RepeatUtil.pm line 78. BEGIN failed--compilation aborted at /work/LAS/mhufford-lab/oushujun/bin/RepeatModeler/RepeatUtil.pm line 78. Compilation failed in require at ./RepeatModeler line 126. BEGIN failed--compilation aborted at ./RepeatModeler line 126.

At this point I am not sure if a special RMBlast is required or something wrong with the configure script.

Thanks, Shujun

jebrosen commented 4 years ago

In RepeatModeler 2.0.1 we had to drop support for RMBlast older than 2.9.0. It should work fine with 2.9.0(-p2) and 2.10.0.

all indicated succeed by the configure script but then dropped (shown un-configured when trying to re-configure).

We recently got a report of this by e-mail as well. Re-running the configure program "forgets" the configured search engines. To verify that the paths have been set, you can check them in RepModelConfig.pm instead of re-running configure.

./RepeatModeler Can't locate WUBlastSearchEngine.pm

This error occurs because RepeatModeler uses perl modules from RepeatMasker, which is why it needs to know the RepeatMasker directory. However none of the directories in @inc looks like a RepeatMasker directory - if you installed RepeatMasker through conda, the correct directory would be something like .../conda/.../share/RepeatMasker/. It looks like you might have specified /home/oushujun/las/bin/miniconda2/envs/EDTA/bin as the path to RepeatMasker, which would have "tricked" configure into accepting it incorrectly.

We should fix configure so that it looks for some of those perl modules, not just the main RepeatMasker script to avoid that in the future.

oushujun commented 4 years ago

Fixing the RepeatMasker path works (with RMBlast v2.9.0).

I got the path /home/oushujun/las/bin/miniconda2/envs/EDTA/bin of the conda-installed RepeatMasker using which RepeatMasker. It went through the configure script check but reported error by the program. By changing the RepeatMasker path to this one /home/oushujun/las/bin/miniconda2/envs/EDTA/share/RepeatMasker/, it works.

I agree that the configure script should also look for the dependent Perl modules from the user provided RepeatMasker path.

splaisan commented 11 months ago

HI, I am trying to install RepeatModeler in conda as the dfam/tetools:latest docker image only works as root and does not allow -u "$(id -u):$(id -g)"

conda create -n repeatmodeler
conda activate repeatmodeler
conda install -c bioconda repeatmodeler

I get a lot of error messages suggesting multiple package source conflicts

Channels:
 - bioconda
 - defaults
 - conda-forge
 - r
 - anaconda
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /opt/miniconda3/envs/repeatmodeler

  added / updated specs:
    - repeatmodeler

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-4.5-2_gnu 
  biopython          pkgs/main/linux-64::biopython-1.78-py39h7f8727e_0 
  blas               pkgs/main/linux-64::blas-1.0-openblas 
  blast              bioconda/linux-64::blast-2.15.0-pl5321h6f7f691_1 
  bz2file            pkgs/main/linux-64::bz2file-0.98-py39h06a4308_1 
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 
  c-ares             pkgs/main/linux-64::c-ares-1.19.1-h5eee18b_0 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.08.22-h06a4308_0 
  cairo              pkgs/main/linux-64::cairo-1.16.0-hb05425b_5 
  cd-hit             bioconda/linux-64::cd-hit-4.8.1-h43eeafb_9 
  curl               pkgs/main/linux-64::curl-8.2.1-h37d81fd_0 
  drmaa              pkgs/main/linux-64::drmaa-0.7.9-py39h06a4308_0 
  entrez-direct      bioconda/linux-64::entrez-direct-16.2-he881be0_1 
  expat              pkgs/main/linux-64::expat-2.5.0-h6a678d5_0 
  font-ttf-dejavu-s~ pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0 
  font-ttf-inconsol~ pkgs/main/noarch::font-ttf-inconsolata-2.001-hcb22688_0 
  font-ttf-source-c~ pkgs/main/noarch::font-ttf-source-code-pro-2.030-hd3eb1b0_0 
  font-ttf-ubuntu    pkgs/main/noarch::font-ttf-ubuntu-0.83-h8b1ccd4_0 
  fontconfig         conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0 
  fonts-anaconda     pkgs/main/noarch::fonts-anaconda-1-h8fa9717_0 
  fonts-conda-ecosy~ pkgs/main/noarch::fonts-conda-ecosystem-1-hd3eb1b0_0 
  freetype           pkgs/main/linux-64::freetype-2.12.1-h4a9f257_0 
  fribidi            pkgs/main/linux-64::fribidi-1.0.10-h7b6447c_0 
  gawk               pkgs/main/linux-64::gawk-5.1.0-h7b6447c_0 
  genometools-genom~ bioconda/linux-64::genometools-genometools-1.6.4-py39h58cc16e_0 
  gettext            conda-forge/linux-64::gettext-0.21.1-h27087fc_0 
  glib               conda-forge/linux-64::glib-2.78.1-hfc55251_1 
  glib-tools         conda-forge/linux-64::glib-tools-2.78.1-hfc55251_1 
  graphite2          pkgs/main/linux-64::graphite2-1.3.14-h295c915_1 
  h5py               pkgs/main/linux-64::h5py-3.9.0-py39he06866b_0 
  harfbuzz           conda-forge/linux-64::harfbuzz-6.0.0-h8e241bc_0 
  hdf5               pkgs/main/linux-64::hdf5-1.12.1-h70be1eb_2 
  hmmer              bioconda/linux-64::hmmer-3.4-hdbdd923_0 
  icu                conda-forge/linux-64::icu-70.1-h27087fc_0 
  krb5               pkgs/main/linux-64::krb5-1.20.1-h568e23c_1 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 
  libcurl            pkgs/main/linux-64::libcurl-8.2.1-h91b91d3_0 
  libedit            pkgs/main/linux-64::libedit-3.1.20221030-h5eee18b_0 
  libev              pkgs/main/linux-64::libev-4.33-h7f8727e_1 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_3 
  libgfortran-ng     pkgs/main/linux-64::libgfortran-ng-11.2.0-h00389a5_1 
  libgfortran5       pkgs/main/linux-64::libgfortran5-11.2.0-h1234567_1 
  libglib            conda-forge/linux-64::libglib-2.78.1-h783c2da_1 
  libgomp            conda-forge/linux-64::libgomp-13.2.0-h807b86a_3 
  libiconv           conda-forge/linux-64::libiconv-1.17-h166bdaf_0 
  libidn2            pkgs/main/linux-64::libidn2-2.3.4-h5eee18b_0 
  libnghttp2         pkgs/main/linux-64::libnghttp2-1.52.0-ha637b67_1 
  libnsl             pkgs/main/linux-64::libnsl-2.0.0-h5eee18b_0 
  libopenblas        pkgs/main/linux-64::libopenblas-0.3.21-h043d6bf_0 
  libpng             pkgs/main/linux-64::libpng-1.6.39-h5eee18b_0 
  libsqlite          conda-forge/linux-64::libsqlite-3.44.2-h2797004_0 
  libssh2            pkgs/main/linux-64::libssh2-1.10.0-h37d81fd_2 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_3 
  libunistring       pkgs/main/linux-64::libunistring-0.9.10-h27cfd23_0 
  libuuid            conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0 
  libxcb             pkgs/main/linux-64::libxcb-1.15-h7f8727e_0 
  libxml2            conda-forge/linux-64::libxml2-2.9.14-h22db469_4 
  libzlib            conda-forge/linux-64::libzlib-1.2.13-hd590300_5 
  ltr_retriever      bioconda/noarch::ltr_retriever-2.9.4-hdfd78af_0 
  mafft              bioconda/linux-64::mafft-7.520-h031d066_3 
  mysql-connector-c  pkgs/main/linux-64::mysql-connector-c-6.1.11-h24aacaa_2 
  ncbi-vdb           bioconda/linux-64::ncbi-vdb-3.0.9-hdbdd923_0 
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 
  ninja-nj           bioconda/linux-64::ninja-nj-0.98-h4ac6f70_3 
  nseg               bioconda/linux-64::nseg-1.0.1-h031d066_4 
  numpy              pkgs/main/linux-64::numpy-1.26.0-py39heeff2f4_0 
  numpy-base         pkgs/main/linux-64::numpy-base-1.26.0-py39h8a23956_0 
  openssl            pkgs/main/linux-64::openssl-1.1.1w-h7f8727e_0 
  ossuuid            conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000 
  pango              conda-forge/linux-64::pango-1.50.14-hd33c08f_0 
  pcre               pkgs/main/linux-64::pcre-8.45-h295c915_0 
  pcre2              pkgs/main/linux-64::pcre2-10.42-hebb0a14_0 
  perl               pkgs/main/linux-64::perl-5.32.1-0_h5eee18b_perl5 
  perl-alien-build   bioconda/linux-64::perl-alien-build-2.48-pl5321hec16e2b_0 
  perl-alien-libxml2 bioconda/linux-64::perl-alien-libxml2-0.17-pl5321hec16e2b_0 
  perl-archive-tar   bioconda/noarch::perl-archive-tar-2.40-pl5321hdfd78af_0 
  perl-base          bioconda/noarch::perl-base-2.23-pl5321hdfd78af_2 
  perl-business-isbn bioconda/noarch::perl-business-isbn-3.007-pl5321hdfd78af_0 
  perl-business-isb~ bioconda/noarch::perl-business-isbn-data-20210112.006-pl5321hdfd78af_0 
  perl-capture-tiny  bioconda/noarch::perl-capture-tiny-0.48-pl5321hdfd78af_2 
  perl-carp          bioconda/noarch::perl-carp-1.38-pl5321hdfd78af_4 
  perl-common-sense  bioconda/noarch::perl-common-sense-3.75-pl5321hdfd78af_0 
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-bzip2-2.201-pl5321h87f3376_1 
  perl-compress-raw~ bioconda/linux-64::perl-compress-raw-zlib-2.105-pl5321h87f3376_0 
  perl-constant      bioconda/noarch::perl-constant-1.33-pl5321hdfd78af_2 
  perl-data-dumper   bioconda/linux-64::perl-data-dumper-2.183-pl5321hec16e2b_1 
  perl-devel-size    bioconda/linux-64::perl-devel-size-0.83-pl5321h031d066_4 
  perl-digest-hmac   bioconda/noarch::perl-digest-hmac-1.04-pl5321hdfd78af_0 
  perl-digest-md5    bioconda/linux-64::perl-digest-md5-2.58-pl5321hec16e2b_1 
  perl-encode        bioconda/linux-64::perl-encode-3.19-pl5321hec16e2b_1 
  perl-encode-locale bioconda/noarch::perl-encode-locale-1.05-pl5321hdfd78af_7 
  perl-exporter      bioconda/noarch::perl-exporter-5.72-pl5321hdfd78af_2 
  perl-exporter-tiny bioconda/noarch::perl-exporter-tiny-1.002002-pl5321hdfd78af_0 
  perl-extutils-mak~ conda-forge/noarch::perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0 
  perl-ffi-checklib  bioconda/noarch::perl-ffi-checklib-0.28-pl5321hdfd78af_0 
  perl-file-chdir    bioconda/noarch::perl-file-chdir-0.1010-pl5321hdfd78af_3 
  perl-file-listing  bioconda/noarch::perl-file-listing-6.16-pl5321hdfd78af_0 
  perl-file-path     conda-forge/noarch::perl-file-path-2.18-pl5321hd8ed1ab_0 
  perl-file-spec     bioconda/noarch::perl-file-spec-3.48_01-pl5321hdfd78af_2 
  perl-file-temp     conda-forge/noarch::perl-file-temp-0.2304-pl5321hd8ed1ab_0 
  perl-file-which    conda-forge/noarch::perl-file-which-1.24-pl5321hd8ed1ab_0 
  perl-html-parser   bioconda/linux-64::perl-html-parser-3.81-pl5321h4ac6f70_1 
  perl-html-tagset   bioconda/noarch::perl-html-tagset-3.20-pl5321hdfd78af_4 
  perl-http-cookies  bioconda/noarch::perl-http-cookies-6.10-pl5321hdfd78af_0 
  perl-http-daemon   bioconda/noarch::perl-http-daemon-6.16-pl5321hdfd78af_0 
  perl-http-date     bioconda/noarch::perl-http-date-6.06-pl5321hdfd78af_0 
  perl-http-message  bioconda/noarch::perl-http-message-6.36-pl5321hdfd78af_0 
  perl-http-negotia~ bioconda/noarch::perl-http-negotiate-6.01-pl5321hdfd78af_4 
  perl-importer      bioconda/noarch::perl-importer-0.026-pl5321hdfd78af_0 
  perl-io-compress   bioconda/linux-64::perl-io-compress-2.201-pl5321hdbdd923_2 
  perl-io-html       bioconda/noarch::perl-io-html-1.004-pl5321hdfd78af_0 
  perl-io-socket-ssl bioconda/noarch::perl-io-socket-ssl-2.074-pl5321hdfd78af_0 
  perl-io-zlib       bioconda/noarch::perl-io-zlib-1.14-pl5321hdfd78af_0 
  perl-json          bioconda/noarch::perl-json-4.10-pl5321hdfd78af_0 
  perl-json-xs       bioconda/linux-64::perl-json-xs-2.34-pl5321h4ac6f70_6 
  perl-libwww-perl   bioconda/noarch::perl-libwww-perl-6.67-pl5321hdfd78af_0 
  perl-list-moreuti~ bioconda/noarch::perl-list-moreutils-0.430-pl5321hdfd78af_0 
  perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.430-pl5321h031d066_2 
  perl-lwp-mediatyp~ bioconda/noarch::perl-lwp-mediatypes-6.04-pl5321hdfd78af_1 
  perl-mime-base64   bioconda/linux-64::perl-mime-base64-3.16-pl5321hec16e2b_2 
  perl-net-http      bioconda/noarch::perl-net-http-6.22-pl5321hdfd78af_0 
  perl-net-ssleay    bioconda/linux-64::perl-net-ssleay-1.92-pl5321h0e0aaa8_1 
  perl-ntlm          bioconda/noarch::perl-ntlm-1.09-pl5321hdfd78af_5 
  perl-parent        bioconda/noarch::perl-parent-0.236-pl5321hdfd78af_2 
  perl-path-tiny     bioconda/noarch::perl-path-tiny-0.122-pl5321hdfd78af_0 
  perl-pathtools     bioconda/linux-64::perl-pathtools-3.75-pl5321hec16e2b_3 
  perl-scalar-list-~ bioconda/linux-64::perl-scalar-list-utils-1.62-pl5321hec16e2b_1 
  perl-scope-guard   bioconda/noarch::perl-scope-guard-0.21-pl5321hdfd78af_3 
  perl-socket        bioconda/linux-64::perl-socket-2.027-pl5321h031d066_4 
  perl-storable      bioconda/linux-64::perl-storable-3.15-pl5321hec16e2b_3 
  perl-sub-info      bioconda/noarch::perl-sub-info-0.002-pl5321hdfd78af_1 
  perl-term-table    bioconda/noarch::perl-term-table-0.016-pl5321hdfd78af_0 
  perl-test-simple   bioconda/noarch::perl-test-simple-1.302190-pl5321hdfd78af_0 
  perl-test2-suite   bioconda/noarch::perl-test2-suite-0.000145-pl5321hdfd78af_0 
  perl-text-soundex  conda-forge/noarch::perl-text-soundex-3.05-pl5321hd8ed1ab_1001 
  perl-time-local    bioconda/noarch::perl-time-local-1.35-pl5321hdfd78af_0 
  perl-timedate      bioconda/noarch::perl-timedate-2.33-pl5321hdfd78af_2 
  perl-try-tiny      bioconda/noarch::perl-try-tiny-0.31-pl5321hdfd78af_1 
  perl-types-serial~ bioconda/noarch::perl-types-serialiser-1.01-pl5321hdfd78af_0 
  perl-uri           bioconda/noarch::perl-uri-5.12-pl5321hdfd78af_0 
  perl-url-encode    bioconda/linux-64::perl-url-encode-0.03-pl5321h9ee0642_0 
  perl-www-robotrul~ bioconda/noarch::perl-www-robotrules-6.02-pl5321hdfd78af_4 
  perl-xml-libxml    bioconda/linux-64::perl-xml-libxml-2.0207-pl5321h661654b_0 
  perl-xml-namespac~ bioconda/noarch::perl-xml-namespacesupport-1.12-pl5321hdfd78af_1 
  perl-xml-sax       bioconda/noarch::perl-xml-sax-1.02-pl5321hdfd78af_1 
  perl-xml-sax-base  bioconda/noarch::perl-xml-sax-base-1.09-pl5321hdfd78af_1 
  pip                pkgs/main/linux-64::pip-23.3.1-py39h06a4308_0 
  pixman             pkgs/main/linux-64::pixman-0.40.0-h7f8727e_1 
  pp                 bioconda/noarch::pp-1.6.4.4-py_0 
  python             pkgs/main/linux-64::python-3.9.18-h7a1cb2a_0 
  python_abi         conda-forge/linux-64::python_abi-3.9-2_cp39 
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 
  recon              bioconda/linux-64::recon-1.08-h031d066_6 
  repeatmasker       bioconda/noarch::repeatmasker-4.1.5-pl5321hdfd78af_1 
  repeatmodeler      bioconda/noarch::repeatmodeler-2.0.5-pl5321hdfd78af_0 
  repeatscout        bioconda/linux-64::repeatscout-1.0.6-hec16e2b_3 
  rmblast            bioconda/linux-64::rmblast-2.14.1-h4565617_0 
  setuptools         pkgs/main/linux-64::setuptools-68.0.0-py39h06a4308_0 
  six                pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1 
  sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0 
  tesorter           bioconda/noarch::tesorter-1.4.6-pyhdfd78af_0 
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0 
  trf                bioconda/linux-64::trf-4.09.1-h031d066_4 
  tzdata             pkgs/main/noarch::tzdata-2023c-h04d1e81_0 
  ucsc-fatotwobit    bioconda/linux-64::ucsc-fatotwobit-447-h954228d_0 
  ucsc-twobitinfo    bioconda/linux-64::ucsc-twobitinfo-447-h954228d_0 
  ucsc-twobittofa    bioconda/linux-64::ucsc-twobittofa-447-h954228d_0 
  wget               pkgs/main/linux-64::wget-1.21.4-h91b91d3_1 
  wheel              pkgs/main/linux-64::wheel-0.41.2-py39h06a4308_0 
  xopen              bioconda/noarch::xopen-0.7.3-py_0 
  xorg-kbproto       conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002 
  xorg-libice        conda-forge/linux-64::xorg-libice-1.1.1-hd590300_0 
  xorg-libsm         conda-forge/linux-64::xorg-libsm-1.2.4-h7391055_0 
  xorg-libx11        conda-forge/linux-64::xorg-libx11-1.8.7-h8ee46fc_0 
  xorg-libxext       conda-forge/linux-64::xorg-libxext-1.3.4-h0b41bf4_2 
  xorg-libxrender    conda-forge/linux-64::xorg-libxrender-0.9.11-hd590300_0 
  xorg-renderproto   conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002 
  xorg-xextproto     conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003 
  xorg-xproto        pkgs/main/linux-64::xorg-xproto-7.0.31-h27cfd23_1007 
  xz                 pkgs/main/linux-64::xz-5.4.2-h5eee18b_0 
  zlib               conda-forge/linux-64::zlib-1.2.13-hd590300_5 

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: \ 
SafetyError: The package for repeatmasker located at /opt/miniconda3/pkgs/repeatmasker-4.1.5-pl5321hdfd78af_1
appears to be corrupted. The path 'share/RepeatMasker/Libraries/Dfam.h5'
has an incorrect size.
  reported size: 68 bytes
  actual size: 1593452770 bytes

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0, conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  path: 'lib/libuuid.a'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0, conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  path: 'lib/libuuid.so'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0, conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  path: 'lib/pkgconfig/uuid.pc'

ClobberError: This transaction has incompatible packages due to a shared path.
  packages: conda-forge/linux-64::libsqlite-3.44.2-h2797004_0, defaults/linux-64::sqlite-3.41.2-h5eee18b_0
  path: 'include/sqlite3.h'

can you please help me thanks