From 66fa4713257ab8cf6f86648c99ee8918c6e47f6f Mon Sep 17 00:00:00 2001
From: iquasere <maildosequeira@gmail.com>
Date: Fri, 28 Apr 2023 14:03:37 +0100
Subject: [PATCH] Updated bioconda integration

---
 .github/workflows/main.yml             |   6 +-
 build.sh                               |  12 +--
 resources/{logo.txt => mosca_logo.txt} |   0
 resources/tools_for_versions.txt       |  40 --------
 workflow/envs/assembly.yaml            | 123 +++++++++++++------------
 workflow/envs/keggcharter.yaml         | 101 ++++++++++----------
 workflow/envs/recognizer.yaml          |  77 ++++++++--------
 workflow/envs/upimapi.yaml             | 118 ++++++++++++++----------
 8 files changed, 230 insertions(+), 247 deletions(-)
 rename resources/{logo.txt => mosca_logo.txt} (100%)
 delete mode 100644 resources/tools_for_versions.txt

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 359aa33..6086087 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -40,7 +40,7 @@ jobs:
           name: mosca
           path: /tmp/mosca.tar
 
-  mgmt_workflow:
+  mgmt-workflow:
     runs-on: ubuntu-latest
     needs: build
     steps:
@@ -61,7 +61,7 @@ jobs:
       - name: MGMT workflow
         run: docker run mosca /bin/bash -c "mosca -c MOSCARDO/configs/mgmt_config.json"
 
-  mgmp_workflow:
+  mgmp-workflow:
     runs-on: ubuntu-latest
     needs: build
     steps:
@@ -85,4 +85,4 @@ jobs:
       - name: MGMP workflow
         run: >
           docker run -v named_volume:/data -v /var/run/docker.sock:/var/run/docker.sock mosca /bin/bash
-          -c "mosca -c MOSCARDO/configs/mgmp_config.json; rm -r output"
+          -c "mosca -c MOSCARDO/configs/mgmp_config.json; du -sh output/*; df -h"
diff --git a/build.sh b/build.sh
index 33fb698..f3eab40 100644
--- a/build.sh
+++ b/build.sh
@@ -1,7 +1,5 @@
-dir="${PREFIX}/share/MOSCA"
-mkdir -p "${dir}/scripts" "${PREFIX}/bin"
-cp workflow/scripts/* "${dir}/scripts"
-cp workflow/Snakefile workflow/mosca.py "${dir}/scripts"
-cp -r resources "${dir}/resources"
-chmod +x "${dir}/scripts/mosca.py"
-ln -s "${dir}/scripts/mosca.py" "${PREFIX}/bin/"
\ No newline at end of file
+echo "Storing MOSCA's files in the Conda environment at: ${PREFIX}"
+mkdir -p "${PREFIX}/share/MOSCA" "${PREFIX}/bin"
+cp -r MOSCA/workflow/* "${PREFIX}/share/MOSCA"
+chmod +x "${PREFIX}/share/MOSCA/mosca.py"
+ln -s "${PREFIX}/share/MOSCA/mosca.py" "${PREFIX}/bin/mosca"
\ No newline at end of file
diff --git a/resources/logo.txt b/resources/mosca_logo.txt
similarity index 100%
rename from resources/logo.txt
rename to resources/mosca_logo.txt
diff --git a/resources/tools_for_versions.txt b/resources/tools_for_versions.txt
deleted file mode 100644
index 88608fa..0000000
--- a/resources/tools_for_versions.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-python
-fastqc
-sortmerna
-seqtk
-trimmomatic
-megahit
-spades
-fraggenescan
-diamond
-upimapi
-htseq
-bowtie2
-maxbin2
-checkm-genome
-bioconductor-deseq2
-bioconductor-edger
-r-pheatmap
-r-optparse
-blast
-krona
-seqkit
-svn
-reportlab
-openpyxl
-xlrd
-r-rcolorbrewer
-pandas
-scikit-learn
-lxml
-biopython
-perl
-progressbar33
-tqdm
-xlsxwriter
-recognizer
-maxquant
-quast
-unzip
-keggcharter
-samtools
\ No newline at end of file
diff --git a/workflow/envs/assembly.yaml b/workflow/envs/assembly.yaml
index 6b93243..f8f2345 100644
--- a/workflow/envs/assembly.yaml
+++ b/workflow/envs/assembly.yaml
@@ -1,7 +1,8 @@
-name: mosca_ass
+name: assembly
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - anaconda
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
@@ -10,7 +11,7 @@ dependencies:
   - alsa-lib=1.2.8=h166bdaf_0
   - bedtools=2.30.0=h468198e_3
   - blast=2.13.0=hf3cf87c_0
-  - bowtie2=2.5.0=py310h8d7afc0_0
+  - bowtie2=2.5.1=py310h8d7afc0_0
   - brotli=1.0.9=h166bdaf_8
   - brotli-bin=1.0.9=h166bdaf_8
   - bwa=0.7.17=h7132678_9
@@ -19,35 +20,39 @@ dependencies:
   - ca-certificates=2022.12.7=ha878542_0
   - cairo=1.16.0=ha61ee94_1014
   - certifi=2022.12.7=pyhd8ed1ab_0
-  - circos=0.69.8=hdfd78af_1
+  - circos=0.69.9=hdfd78af_0
   - colorama=0.4.6=pyhd8ed1ab_0
-  - curl=7.87.0=hdc1c0ab_0
+  - contourpy=1.0.7=py310hdf3cbec_0
+  - curl=7.87.0=h6312ad2_0
   - cycler=0.11.0=pyhd8ed1ab_0
   - entrez-direct=16.2=he881be0_1
-  - expat=2.5.0=h27087fc_0
+  - expat=2.5.0=hcb278e6_1
   - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
   - font-ttf-inconsolata=3.000=h77eed37_0
   - font-ttf-source-code-pro=2.038=h77eed37_0
   - font-ttf-ubuntu=0.83=hab24e00_0
-  - fontconfig=2.14.1=hc2a2eb6_0
+  - fontconfig=2.14.2=h14ed4e7_0
   - fonts-conda-ecosystem=1=0
   - fonts-conda-forge=1=0
+  - fonttools=4.39.3=py310h1fa729e_0
   - freetype=2.12.1=hca18f0e_1
   - gettext=0.21.1=h27087fc_0
-  - giflib=5.2.1=h36c2ea0_2
+  - giflib=5.2.1=h0b41bf4_3
   - glimmerhmm=3.0.4=pl5321h87f3376_5
   - gmcloser=1.6.2=hdfd78af_1
   - graphite2=1.3.13=h58526e2_1001
   - harfbuzz=6.0.0=h8e241bc_0
+  - htslib=1.17=h6bc39ce_0
   - icu=70.1=h27087fc_0
   - joblib=1.2.0=pyhd8ed1ab_0
-  - jpeg=9e=h166bdaf_2
+  - jpeg=9e=h0b41bf4_3
   - k8=0.2.5=hd03093a_2
   - kernel-headers_linux-64=3.10.0=h4a8ded7_13
   - keyutils=1.6.1=h166bdaf_0
-  - krb5=1.20.1=h81ceb04_0
-  - lcms2=2.14=hfd0df8a_1
-  - ld_impl_linux-64=2.39=hcc3a1bd_1
+  - kiwisolver=1.4.4=py310hbf28c38_1
+  - krb5=1.20.1=hf9c8cef_0
+  - lcms2=2.14=h6ed2654_0
+  - ld_impl_linux-64=2.40=h41732ed_0
   - lerc=4.0.0=h27087fc_0
   - libblas=3.9.0=16_linux64_openblas
   - libbrotlicommon=1.0.9=h166bdaf_8
@@ -55,48 +60,51 @@ dependencies:
   - libbrotlienc=1.0.9=h166bdaf_8
   - libcblas=3.9.0=16_linux64_openblas
   - libcups=2.3.3=h36d4200_3
-  - libcurl=7.87.0=hdc1c0ab_0
-  - libdeflate=1.14=h166bdaf_0
+  - libcurl=7.87.0=h6312ad2_0
+  - libdeflate=1.13=h166bdaf_0
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=h516909a_1
+  - libexpat=2.5.0=hcb278e6_1
   - libffi=3.4.2=h7f98852_5
   - libgcc-ng=12.2.0=h65d4601_19
-  - libgd=2.3.3=h5aea950_4
+  - libgd=2.3.3=h18fbbfe_3
   - libgfortran-ng=12.2.0=h69a702a_19
   - libgfortran5=12.2.0=h337968e_19
-  - libglib=2.74.1=h606061b_1
+  - libglib=2.76.2=hebfc3b9_0
   - libgomp=12.2.0=h65d4601_19
-  - libhwloc=2.8.0=h32351e8_1
+  - libhwloc=2.9.1=hd6dc26d_0
   - libiconv=1.17=h166bdaf_0
   - libidn2=2.3.4=h166bdaf_0
   - liblapack=3.9.0=16_linux64_openblas
-  - libnghttp2=1.47.0=hff17c54_1
+  - libnghttp2=1.51.0=hdcd2b5c_0
   - libnsl=2.0.0=h7f98852_0
   - libopenblas=0.3.21=pthreads_h78a6416_3
   - libpng=1.6.39=h753d276_0
-  - libsqlite=3.40.0=h753d276_0
-  - libssh2=1.10.0=hf14f497_3
+  - libsqlite=3.40.0=h753d276_1
+  - libssh2=1.10.0=haa6b8db_3
   - libstdcxx-ng=12.2.0=h46fd767_19
-  - libtiff=4.5.0=h82bc61c_0
+  - libtiff=4.4.0=h0e0dad5_3
   - libunistring=0.9.10=h7f98852_0
-  - libuuid=2.32.1=h7f98852_1000
-  - libwebp=1.2.4=h1daa5a0_1
+  - libuuid=2.38.1=h0b41bf4_0
+  - libwebp=1.2.4=h522a892_0
   - libwebp-base=1.2.4=h166bdaf_0
   - libxcb=1.13=h7f98852_1004
-  - libxml2=2.10.3=h7463322_0
+  - libxml2=2.10.3=hca2bb57_4
   - libzlib=1.2.13=h166bdaf_4
   - llvm-openmp=8.0.1=hc9558a2_0
-  - matplotlib-base=3.6.2=py310h8d5ebf3_0
-  - megahit=1.2.9=h2e03b76_1
-  - minimap2=2.24=h7132678_1
+  - matplotlib-base=3.7.1=py310he60537e_0
+  - megahit=1.2.9=h5b5514e_2
+  - minimap2=2.25=h7132678_0
   - mummer=3.23=pl5321h87f3376_14
   - munkres=1.1.4=pyh9f0ad1d_0
   - ncurses=6.3=h27087fc_1
+  - numpy=1.24.3=py310ha4c1d20_0
   - openjdk=17.0.3=h58dac75_5
-  - openjpeg=2.5.0=hfec8fc6_2
+  - openjpeg=2.5.0=h7d73246_1
   - openmp=8.0.1=0
-  - openssl=3.0.7=h0b41bf4_1
-  - packaging=22.0=pyhd8ed1ab_0
+  - openssl=1.1.1t=h0b41bf4_0
+  - packaging=23.1=pyhd8ed1ab_0
+  - pandas=2.0.1=py310h7cbd5c2_0
   - pcre=8.45=h9c3ff4c_0
   - pcre2=10.40=hc3806b6_0
   - perl=5.32.1=2_h7f98852_perl5
@@ -115,7 +123,7 @@ dependencies:
   - perl-extutils-config=0.008=pl5321ha770c72_0
   - perl-extutils-helpers=0.026=pl5321ha770c72_0
   - perl-extutils-installpaths=0.012=pl5321ha770c72_0
-  - perl-extutils-makemaker=7.66=pl5321hd8ed1ab_0
+  - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
   - perl-extutils-pl2bat=0.005=pl5321ha770c72_0
   - perl-findbin=1.51=pl5321hdfd78af_3
   - perl-font-ttf=1.06=pl5321hdfd78af_1
@@ -124,7 +132,7 @@ dependencies:
   - perl-inc-latest=0.500=pl5321ha770c72_0
   - perl-io-compress=2.201=pl5321h87f3376_0
   - perl-io-string=1.08=pl5321hdfd78af_4
-  - perl-io-zlib=1.11=pl5321hdfd78af_0
+  - perl-io-zlib=1.14=pl5321hdfd78af_0
   - perl-json=4.10=pl5321hdfd78af_0
   - perl-json-xs=2.34=pl5321h9f5acd7_5
   - perl-list-moreutils=0.430=pl5321hdfd78af_0
@@ -138,7 +146,7 @@ dependencies:
   - perl-module-runtime=0.016=pl5321ha770c72_0
   - perl-number-format=1.75=pl5321hdfd78af_4
   - perl-params-validate=1.31=pl5321hec16e2b_0
-  - perl-parent=0.239=pl5321hd8ed1ab_0
+  - perl-parent=0.241=pl5321hd8ed1ab_0
   - perl-pathtools=3.75=pl5321h166bdaf_0
   - perl-pod-escapes=1.07=pl5321hdfd78af_2
   - perl-pod-usage=2.03=pl5321hdfd78af_0
@@ -157,55 +165,50 @@ dependencies:
   - perl-try-tiny=0.31=pl5321ha770c72_0
   - perl-types-serialiser=1.01=pl5321hdfd78af_0
   - perl-xml-parser=2.44_01=pl5321hc3e0081_1003
-  - pip=22.3.1=pyhd8ed1ab_0
+  - pillow=9.2.0=py310h454ad03_3
+  - pip=23.1.2=pyhd8ed1ab_0
   - pixman=0.40.0=h36c2ea0_0
+  - psutil=5.9.5=py310h1fa729e_0
   - pthread-stubs=0.4=h36c2ea0_1001
   - pyparsing=3.0.9=pyhd8ed1ab_0
-  - python=3.10.8=h4a9ceb5_0_cpython
+  - python=3.10.8=h257c98d_0_cpython
   - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-tzdata=2023.3=pyhd8ed1ab_0
   - python_abi=3.10=3_cp310
-  - pytz=2022.7=pyhd8ed1ab_0
-  - readline=8.1.2=h0f457ee_0
-  - setuptools=65.6.3=pyhd8ed1ab_0
+  - pytz=2023.3=pyhd8ed1ab_0
+  - quast=5.2.0=py310pl5321hc8f18ef_2
+  - readline=8.2=h8228510_1
+  - samtools=1.17=h00cdaf9_0
+  - setuptools=67.7.2=pyhd8ed1ab_0
+  - simplejson=3.19.1=py310h1fa729e_0
   - six=1.16.0=pyh6c4a22f_0
   - spades=3.15.5=h95f258a_1
   - sysroot_linux-64=2.17=h4a8ded7_13
-  - tbb=2021.7.0=h924138e_1
+  - tbb=2021.9.0=hf52228f_0
   - tk=8.6.12=h27826a3_0
-  - tqdm=4.64.1=pyhd8ed1ab_0
-  - tzdata=2022g=h191b570_0
-  - wget=1.20.3=ha35d2d1_1
-  - wheel=0.38.4=pyhd8ed1ab_0
+  - tqdm=4.65.0=pyhd8ed1ab_1
+  - tzdata=2023c=h71feb2d_0
+  - unicodedata2=15.0.0=py310h5764c6d_0
+  - wget=1.20.3=ha56f1ee_1
+  - wheel=0.40.0=pyhd8ed1ab_0
   - xorg-fixesproto=5.0=h7f98852_1002
   - xorg-inputproto=2.3.2=h7f98852_1002
   - xorg-kbproto=1.0.7=h7f98852_1002
   - xorg-libice=1.0.10=h7f98852_0
   - xorg-libsm=1.2.3=hd9c2040_1000
-  - xorg-libx11=1.7.2=h7f98852_0
+  - xorg-libx11=1.8.4=h0b41bf4_0
   - xorg-libxau=1.0.9=h7f98852_0
   - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xorg-libxext=1.3.4=h7f98852_1
+  - xorg-libxext=1.3.4=h0b41bf4_2
   - xorg-libxfixes=5.0.3=h7f98852_1004
   - xorg-libxi=1.7.10=h7f98852_0
   - xorg-libxrender=0.9.10=h7f98852_1003
   - xorg-libxtst=1.2.3=h7f98852_1002
   - xorg-recordproto=1.14.2=h7f98852_1002
   - xorg-renderproto=0.11.1=h7f98852_1002
-  - xorg-xextproto=7.3.0=h7f98852_1002
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
   - xorg-xproto=7.0.31=h7f98852_1007
   - xz=5.2.6=h166bdaf_0
   - zlib=1.2.13=h166bdaf_4
-  - zstd=1.5.2=h6239696_4
-  - pip:
-    - contourpy==1.0.6
-    - fonttools==4.38.0
-    - kiwisolver==1.4.4
-    - matplotlib==3.6.2
-    - numpy==1.24.0
-    - pandas==1.5.2
-    - pillow==9.2.0
-    - psutil==5.9.4
-    - quast==5.2.0
-    - simplejson==3.18.0
-    - unicodedata2==15.0.0
-prefix: /opt/conda/envs/my_env
+  - zstd=1.5.2=h3eb15da_6
+prefix: /opt/conda/envs/assembly
diff --git a/workflow/envs/keggcharter.yaml b/workflow/envs/keggcharter.yaml
index 6c44491..5a5b351 100644
--- a/workflow/envs/keggcharter.yaml
+++ b/workflow/envs/keggcharter.yaml
@@ -1,119 +1,120 @@
-name: mosca_kegg
+name: keggcharter
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - anaconda
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=2_gnu
-  - boost-cpp=1.78.0=h75c5d50_1
+  - biopython=1.81=py311h2582759_0
+  - boost-cpp=1.78.0=h6582d0a_3
   - brotli=1.0.9=h166bdaf_8
   - brotli-bin=1.0.9=h166bdaf_8
   - bzip2=1.0.8=h7f98852_4
   - c-ares=1.18.1=h7f98852_0
   - ca-certificates=2022.12.7=ha878542_0
-  - cairo=1.16.0=ha61ee94_1014
+  - cairo=1.16.0=h35add3b_1015
   - certifi=2022.12.7=pyhd8ed1ab_0
   - colorama=0.4.6=pyhd8ed1ab_0
+  - contourpy=1.0.7=py311ha3edf6b_0
   - cycler=0.11.0=pyhd8ed1ab_0
-  - et_xmlfile=1.0.1=py_1001
-  - expat=2.5.0=h27087fc_0
+  - et_xmlfile=1.1.0=pyhd8ed1ab_0
+  - expat=2.5.0=hcb278e6_1
   - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
   - font-ttf-inconsolata=3.000=h77eed37_0
   - font-ttf-source-code-pro=2.038=h77eed37_0
   - font-ttf-ubuntu=0.83=hab24e00_0
-  - fontconfig=2.14.1=hc2a2eb6_0
+  - fontconfig=2.14.2=h14ed4e7_0
   - fonts-conda-ecosystem=1=0
   - fonts-conda-forge=1=0
+  - fonttools=4.39.3=py311h2582759_0
   - freetype=2.12.1=hca18f0e_1
   - gettext=0.21.1=h27087fc_0
-  - icu=70.1=h27087fc_0
-  - jpeg=9e=h166bdaf_2
-  - keggcharter>=0.5
+  - icu=72.1=hcb278e6_0
+  - keggcharter=0.5.0=hdfd78af_0
   - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.4.4=py311h4dd048b_1
   - krb5=1.20.1=h81ceb04_0
-  - lcms2=2.14=hfd0df8a_1
-  - ld_impl_linux-64=2.39=hcc3a1bd_1
+  - lcms2=2.15=haa2dc70_1
+  - ld_impl_linux-64=2.40=h41732ed_0
   - lerc=4.0.0=h27087fc_0
   - libblas=3.9.0=16_linux64_openblas
   - libbrotlicommon=1.0.9=h166bdaf_8
   - libbrotlidec=1.0.9=h166bdaf_8
   - libbrotlienc=1.0.9=h166bdaf_8
   - libcblas=3.9.0=16_linux64_openblas
-  - libcurl=7.87.0=hdc1c0ab_0
-  - libdeflate=1.14=h166bdaf_0
+  - libcurl=8.0.1=h588be90_0
+  - libdeflate=1.18=h0b41bf4_0
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=h516909a_1
+  - libexpat=2.5.0=hcb278e6_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
-  - libglib=2.74.1=h606061b_1
+  - libglib=2.76.1=ha491796_0
   - libgomp=12.2.0=h65d4601_19
   - libiconv=1.17=h166bdaf_0
+  - libjpeg-turbo=2.1.5.1=h0b41bf4_0
   - liblapack=3.9.0=16_linux64_openblas
-  - libnghttp2=1.47.0=hff17c54_1
+  - libnghttp2=1.52.0=h61bc06f_0
   - libnsl=2.0.0=h7f98852_0
   - libopenblas=0.3.21=pthreads_h78a6416_3
   - libpng=1.6.39=h753d276_0
   - libsqlite=3.40.0=h753d276_0
   - libssh2=1.10.0=hf14f497_3
   - libstdcxx-ng=12.2.0=h46fd767_19
-  - libtiff=4.5.0=h82bc61c_0
-  - libuuid=2.32.1=h7f98852_1000
-  - libwebp-base=1.2.4=h166bdaf_0
+  - libtiff=4.5.0=ha587672_6
+  - libuuid=2.38.1=h0b41bf4_0
+  - libwebp-base=1.3.0=h0b41bf4_0
   - libxcb=1.13=h7f98852_1004
   - libzlib=1.2.13=h166bdaf_4
-  - matplotlib-base=3.6.2=py311he728205_0
-  - mscorefonts=0.0.1=2
+  - matplotlib-base=3.7.1=py311h8597a09_0
+  - mscorefonts=0.0.1=3
   - munkres=1.1.4=pyh9f0ad1d_0
   - ncurses=6.3=h27087fc_1
   - nspr=4.35=h27087fc_0
-  - nss=3.82=he02c5a1_0
+  - nss=3.89=he45b914_0
+  - numpy=1.24.2=py311h8e6699e_0
   - openjpeg=2.5.0=hfec8fc6_2
-  - openssl=3.0.7=h0b41bf4_1
-  - packaging=22.0=pyhd8ed1ab_0
+  - openpyxl=3.1.1=py311h2582759_0
+  - openssl=3.1.0=h0b41bf4_0
+  - packaging=23.1=pyhd8ed1ab_0
+  - pandas=2.0.0=py311h2872171_0
   - pcre2=10.40=hc3806b6_0
-  - pip=22.3.1=pyhd8ed1ab_0
+  - pillow=9.5.0=py311h573f0d3_0
+  - pip=23.1=pyhd8ed1ab_0
   - pixman=0.40.0=h36c2ea0_0
-  - poppler=22.12.0=h091648b_1
-  - poppler-data=0.4.11=hd8ed1ab_0
+  - poppler=23.04.0=hf052cbe_1
+  - poppler-data=0.4.12=hd8ed1ab_0
   - pthread-stubs=0.4=h36c2ea0_1001
   - pyparsing=3.0.9=pyhd8ed1ab_0
-  - python=3.11.0=ha86cf86_0_cpython
+  - python=3.11.3=h2755cc3_0_cpython
   - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-tzdata=2023.3=pyhd8ed1ab_0
   - python_abi=3.11=3_cp311
-  - pytz=2022.7=pyhd8ed1ab_0
-  - readline=8.1.2=h0f457ee_0
-  - setuptools=65.6.3=pyhd8ed1ab_0
+  - pytz=2023.3=pyhd8ed1ab_0
+  - readline=8.2=h8228510_1
+  - reportlab=3.6.12=py311h2eb0c47_2
+  - setuptools=67.7.1=pyhd8ed1ab_0
   - six=1.16.0=pyh6c4a22f_0
   - tk=8.6.12=h27826a3_0
-  - tqdm=4.64.1=pyhd8ed1ab_0
-  - tzdata=2022g=h191b570_0
-  - wheel=0.38.4=pyhd8ed1ab_0
+  - tqdm=4.65.0=pyhd8ed1ab_1
+  - tzdata=2023c=h71feb2d_0
+  - wheel=0.40.0=pyhd8ed1ab_0
   - xorg-kbproto=1.0.7=h7f98852_1002
   - xorg-libice=1.0.10=h7f98852_0
   - xorg-libsm=1.2.3=hd9c2040_1000
-  - xorg-libx11=1.7.2=h7f98852_0
+  - xorg-libx11=1.8.4=h0b41bf4_0
   - xorg-libxau=1.0.9=h7f98852_0
   - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xorg-libxext=1.3.4=h7f98852_1
+  - xorg-libxext=1.3.4=h0b41bf4_2
   - xorg-libxrender=0.9.10=h7f98852_1003
   - xorg-renderproto=0.11.1=h7f98852_1002
-  - xorg-xextproto=7.3.0=h7f98852_1002
+  - xorg-xextproto=7.3.0=h0b41bf4_1003
   - xorg-xproto=7.0.31=h7f98852_1007
   - xz=5.2.6=h166bdaf_0
   - zlib=1.2.13=h166bdaf_4
-  - zstd=1.5.2=h6239696_4
-  - pip:
-    - biopython==1.80
-    - contourpy==1.0.6
-    - fonttools==4.38.0
-    - kiwisolver==1.4.4
-    - matplotlib==3.6.2
-    - numpy==1.24.0
-    - openpyxl==3.0.10
-    - pandas==1.5.2
-    - pillow==9.2.0
-    - reportlab==3.6.12
-prefix: /opt/conda/envs/my_env
+  - zstd=1.5.2=h3eb15da_6
+prefix: /opt/conda/envs/keggcharter
diff --git a/workflow/envs/recognizer.yaml b/workflow/envs/recognizer.yaml
index 04a3874..e0be5ca 100644
--- a/workflow/envs/recognizer.yaml
+++ b/workflow/envs/recognizer.yaml
@@ -1,33 +1,38 @@
-name: mosca_recog
+name: recognizer
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - anaconda
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=2_gnu
   - blast=2.13.0=hf3cf87c_0
+  - brotlipy=0.7.0=py311hd4cff14_1005
   - bzip2=1.0.8=h7f98852_4
   - c-ares=1.18.1=h7f98852_0
   - ca-certificates=2022.12.7=ha878542_0
   - certifi=2022.12.7=pyhd8ed1ab_0
-  - charset-normalizer=2.1.1=pyhd8ed1ab_0
+  - cffi=1.15.1=py311h409f033_3
+  - charset-normalizer=3.1.0=pyhd8ed1ab_0
   - colorama=0.4.6=pyhd8ed1ab_0
-  - curl=7.87.0=hdc1c0ab_0
+  - cryptography=40.0.2=py311h9b4c7bb_0
+  - curl=7.88.1=hdc1c0ab_1
   - entrez-direct=16.2=he881be0_1
-  - et_xmlfile=1.0.1=py_1001
+  - et_xmlfile=1.1.0=pyhd8ed1ab_0
   - gettext=0.21.1=h27087fc_0
-  - icu=70.1=h27087fc_0
+  - icu=72.1=hcb278e6_0
   - idna=3.4=pyhd8ed1ab_0
   - keyutils=1.6.1=h166bdaf_0
   - krb5=1.20.1=h81ceb04_0
   - krona=2.8.1=pl5321hdfd78af_1
-  - ld_impl_linux-64=2.39=hcc3a1bd_1
+  - ld_impl_linux-64=2.40=h41732ed_0
   - libblas=3.9.0=16_linux64_openblas
   - libcblas=3.9.0=16_linux64_openblas
-  - libcurl=7.87.0=hdc1c0ab_0
+  - libcurl=7.88.1=hdc1c0ab_1
   - libedit=3.1.20191231=he28a2e2_2
   - libev=4.33=h516909a_1
+  - libexpat=2.5.0=hcb278e6_1
   - libffi=3.4.2=h7f98852_5
   - libgcc-ng=12.2.0=h65d4601_19
   - libgfortran-ng=12.2.0=h69a702a_19
@@ -36,19 +41,23 @@ dependencies:
   - libiconv=1.17=h166bdaf_0
   - libidn2=2.3.4=h166bdaf_0
   - liblapack=3.9.0=16_linux64_openblas
-  - libnghttp2=1.47.0=hff17c54_1
+  - libnghttp2=1.52.0=h61bc06f_0
   - libnsl=2.0.0=h7f98852_0
   - libopenblas=0.3.21=pthreads_h78a6416_3
   - libsqlite=3.40.0=h753d276_0
   - libssh2=1.10.0=hf14f497_3
   - libstdcxx-ng=12.2.0=h46fd767_19
   - libunistring=0.9.10=h7f98852_0
-  - libuuid=2.32.1=h7f98852_1000
-  - libxml2=2.10.3=h7463322_0
+  - libuuid=2.38.1=h0b41bf4_0
+  - libxml2=2.10.4=hfdac1af_0
   - libxslt=1.1.37=h873f0b0_0
   - libzlib=1.2.13=h166bdaf_4
+  - lxml=4.9.2=py311h14a6109_0
   - ncurses=6.3=h27087fc_1
-  - openssl=3.0.7=h0b41bf4_1
+  - numpy=1.24.2=py311h8e6699e_0
+  - openpyxl=3.1.1=py311h2582759_0
+  - openssl=3.1.0=h0b41bf4_0
+  - pandas=2.0.0=py311h2872171_0
   - pcre=8.45=h9c3ff4c_0
   - perl=5.32.1=2_h7f98852_perl5
   - perl-archive-tar=2.40=pl5321hdfd78af_0
@@ -59,46 +68,40 @@ dependencies:
   - perl-encode=3.19=pl5321h166bdaf_0
   - perl-exporter=5.74=pl5321hd8ed1ab_0
   - perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0
-  - perl-extutils-makemaker=7.66=pl5321hd8ed1ab_0
+  - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
   - perl-io-compress=2.201=pl5321h87f3376_0
-  - perl-io-zlib=1.11=pl5321hdfd78af_0
+  - perl-io-zlib=1.14=pl5321hdfd78af_0
   - perl-json=4.10=pl5321hdfd78af_0
   - perl-json-xs=2.34=pl5321h9f5acd7_5
   - perl-list-moreutils=0.430=pl5321hdfd78af_0
   - perl-list-moreutils-xs=0.430=pl5321hec16e2b_1
-  - perl-parent=0.239=pl5321hd8ed1ab_0
+  - perl-parent=0.241=pl5321hd8ed1ab_0
   - perl-pathtools=3.75=pl5321h166bdaf_0
   - perl-scalar-list-utils=1.63=pl5321h166bdaf_0
   - perl-storable=3.15=pl5321h166bdaf_0
   - perl-types-serialiser=1.01=pl5321hdfd78af_0
-  - pip=22.3.1=pyhd8ed1ab_0
+  - pip=23.1=pyhd8ed1ab_0
   - pycparser=2.21=pyhd8ed1ab_0
-  - pyopenssl=22.1.0=pyhd8ed1ab_0
+  - pyopenssl=23.1.1=pyhd8ed1ab_0
   - pysocks=1.7.1=pyha2e5f31_6
-  - python=3.11.0=ha86cf86_0_cpython
+  - python=3.11.3=h2755cc3_0_cpython
   - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-tzdata=2023.3=pyhd8ed1ab_0
   - python_abi=3.11=3_cp311
-  - pytz=2022.7=pyhd8ed1ab_0
-  - readline=8.1.2=h0f457ee_0
-  - recognizer>=1.9
-  - requests=2.28.1=pyhd8ed1ab_1
-  - setuptools=65.6.3=pyhd8ed1ab_0
+  - pytz=2023.3=pyhd8ed1ab_0
+  - readline=8.2=h8228510_1
+  - recognizer=1.9.1=hdfd78af_0
+  - requests=2.28.2=pyhd8ed1ab_1
+  - setuptools=67.7.1=pyhd8ed1ab_0
   - six=1.16.0=pyh6c4a22f_0
   - tk=8.6.12=h27826a3_0
-  - tqdm=4.64.1=pyhd8ed1ab_0
-  - tzdata=2022g=h191b570_0
-  - urllib3=1.26.13=pyhd8ed1ab_0
+  - tqdm=4.65.0=pyhd8ed1ab_1
+  - tzdata=2023c=h71feb2d_0
+  - urllib3=1.26.15=pyhd8ed1ab_0
   - wget=1.20.3=ha35d2d1_1
-  - wheel=0.38.4=pyhd8ed1ab_0
-  - xlsxwriter=3.0.3=pyhd8ed1ab_0
+  - wheel=0.40.0=pyhd8ed1ab_0
+  - xlsxwriter=3.0.9=pyhd8ed1ab_0
   - xz=5.2.6=h166bdaf_0
   - zlib=1.2.13=h166bdaf_4
-  - pip:
-    - brotlipy==0.7.0
-    - cffi==1.15.1
-    - cryptography==38.0.4
-    - lxml==4.9.2
-    - numpy==1.24.0
-    - openpyxl==3.0.10
-    - pandas==1.5.2
-prefix: /opt/conda/envs/my_env
+  - zstd=1.5.2=h3eb15da_6
+prefix: /opt/conda/envs/recognizer
diff --git a/workflow/envs/upimapi.yaml b/workflow/envs/upimapi.yaml
index 66a329a..34eb90e 100644
--- a/workflow/envs/upimapi.yaml
+++ b/workflow/envs/upimapi.yaml
@@ -1,83 +1,101 @@
-name: mosca_upimapi
+name: upimapi
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
+  - anaconda
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=2_gnu
-  - async_generator=1.10=py_0
-  - attrs=22.2.0=pyh71513ae_0
-  - boost-cpp=1.74.0=h75c5d50_8
+  - biopython=1.81=py311h2582759_0
+  - blast=2.13.0=hf3cf87c_0
+  - brotlipy=0.7.0=py311hd4cff14_1005
   - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.18.1=h7f98852_0
   - ca-certificates=2022.12.7=ha878542_0
   - certifi=2022.12.7=pyhd8ed1ab_0
-  - charset-normalizer=2.1.1=pyhd8ed1ab_0
+  - cffi=1.15.1=py311h409f033_3
+  - charset-normalizer=3.1.0=pyhd8ed1ab_0
   - colorama=0.4.6=pyhd8ed1ab_0
-  - diamond=2.0.15=hb97b32f_1
-  - firefox=108.0=hcb278e6_0
-  - geckodriver=0.32.0=h4b87306_0
-  - h11=0.14.0=pyhd8ed1ab_0
-  - icu=70.1=h27087fc_0
+  - cryptography=40.0.2=py311h9b4c7bb_0
+  - curl=7.88.1=hdc1c0ab_1
+  - diamond=2.1.6=h5b5514e_1
+  - entrez-direct=16.2=he881be0_1
+  - gettext=0.21.1=h27087fc_0
   - idna=3.4=pyhd8ed1ab_0
-  - ld_impl_linux-64=2.39=hcc3a1bd_1
+  - keyutils=1.6.1=h166bdaf_0
+  - krb5=1.20.1=h81ceb04_0
+  - ld_impl_linux-64=2.40=h41732ed_0
   - libblas=3.9.0=16_linux64_openblas
   - libcblas=3.9.0=16_linux64_openblas
+  - libcurl=7.88.1=hdc1c0ab_1
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libexpat=2.5.0=hcb278e6_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
-  - libiconv=1.17=h166bdaf_0
+  - libidn2=2.3.4=h166bdaf_0
   - liblapack=3.9.0=16_linux64_openblas
+  - libnghttp2=1.52.0=h61bc06f_0
   - libnsl=2.0.0=h7f98852_0
   - libopenblas=0.3.21=pthreads_h78a6416_3
   - libsqlite=3.40.0=h753d276_0
+  - libssh2=1.10.0=hf14f497_3
   - libstdcxx-ng=12.2.0=h46fd767_19
-  - libuuid=2.32.1=h7f98852_1000
-  - libxml2=2.10.3=h7463322_0
-  - libxslt=1.1.37=h873f0b0_0
+  - libunistring=0.9.10=h7f98852_0
+  - libuuid=2.38.1=h0b41bf4_0
   - libzlib=1.2.13=h166bdaf_4
   - ncurses=6.3=h27087fc_1
-  - openssl=3.0.7=h0b41bf4_1
-  - outcome=1.2.0=pyhd8ed1ab_0
-  - pip=22.3.1=pyhd8ed1ab_0
+  - numpy=1.24.2=py311h8e6699e_0
+  - openssl=3.1.0=h0b41bf4_0
+  - pandas=2.0.0=py311h2872171_0
+  - pcre=8.45=h9c3ff4c_0
+  - perl=5.32.1=2_h7f98852_perl5
+  - perl-archive-tar=2.40=pl5321hdfd78af_0
+  - perl-carp=1.50=pl5321hd8ed1ab_0
+  - perl-common-sense=3.75=pl5321hd8ed1ab_0
+  - perl-compress-raw-bzip2=2.201=pl5321h166bdaf_0
+  - perl-compress-raw-zlib=2.202=pl5321h166bdaf_0
+  - perl-encode=3.19=pl5321h166bdaf_0
+  - perl-exporter=5.74=pl5321hd8ed1ab_0
+  - perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0
+  - perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
+  - perl-io-compress=2.201=pl5321h87f3376_0
+  - perl-io-zlib=1.14=pl5321hdfd78af_0
+  - perl-json=4.10=pl5321hdfd78af_0
+  - perl-json-xs=2.34=pl5321h9f5acd7_5
+  - perl-list-moreutils=0.430=pl5321hdfd78af_0
+  - perl-list-moreutils-xs=0.430=pl5321hec16e2b_1
+  - perl-parent=0.241=pl5321hd8ed1ab_0
+  - perl-pathtools=3.75=pl5321h166bdaf_0
+  - perl-scalar-list-utils=1.63=pl5321h166bdaf_0
+  - perl-storable=3.15=pl5321h166bdaf_0
+  - perl-types-serialiser=1.01=pl5321hdfd78af_0
+  - pip=23.1=pyhd8ed1ab_0
+  - psutil=5.9.5=py311h2582759_0
   - pycparser=2.21=pyhd8ed1ab_0
-  - pyopenssl=22.1.0=pyhd8ed1ab_0
+  - pyopenssl=23.1.1=pyhd8ed1ab_0
   - pysocks=1.7.1=pyha2e5f31_6
-  - python=3.11.0=ha86cf86_0_cpython
+  - python=3.11.3=h2755cc3_0_cpython
   - python-dateutil=2.8.2=pyhd8ed1ab_0
+  - python-tzdata=2023.3=pyhd8ed1ab_0
   - python_abi=3.11=3_cp311
-  - pytz=2022.7=pyhd8ed1ab_0
-  - readline=8.1.2=h0f457ee_0
-  - requests=2.28.1=pyhd8ed1ab_1
-  - selenium=4.7.2=pyhd8ed1ab_0
-  - setuptools=65.6.3=pyhd8ed1ab_0
+  - pytz=2023.3=pyhd8ed1ab_0
+  - readline=8.2=h8228510_1
+  - requests=2.28.2=pyhd8ed1ab_1
+  - setuptools=67.7.1=pyhd8ed1ab_0
   - six=1.16.0=pyh6c4a22f_0
-  - sniffio=1.3.0=pyhd8ed1ab_0
-  - sortedcontainers=2.4.0=pyhd8ed1ab_0
   - tk=8.6.12=h27826a3_0
-  - tqdm=4.64.1=pyhd8ed1ab_0
-  - trio-websocket=0.9.2=pyhd8ed1ab_0
-  - typing_extensions=4.4.0=pyha770c72_0
-  - tzdata=2022g=h191b570_0
-  - upimapi>=1.9
-  - urllib3=1.26.13=pyhd8ed1ab_0
-  - wheel=0.38.4=pyhd8ed1ab_0
-  - wsproto=1.2.0=pyhd8ed1ab_0
+  - tqdm=4.65.0=pyhd8ed1ab_1
+  - tzdata=2023c=h71feb2d_0
+  - upimapi=1.9.0=hdfd78af_0
+  - urllib3=1.26.15=pyhd8ed1ab_0
+  - wget=1.20.3=ha35d2d1_1
+  - wheel=0.40.0=pyhd8ed1ab_0
   - xz=5.2.6=h166bdaf_0
-  - yaml=0.2.5=h7f98852_2
   - zlib=1.2.13=h166bdaf_4
-  - zstd=1.5.2=h6239696_4
-  - pip:
-    - biopython==1.80
-    - brotlipy==0.7.0
-    - cffi==1.15.1
-    - cryptography==38.0.4
-    - lxml==4.9.2
-    - numpy==1.24.0
-    - pandas==1.5.2
-    - psutil==5.9.4
-    - pyyaml==6.0
-    - trio==0.22.0
-prefix: /opt/conda/envs/my_env
+  - zstd=1.5.2=h3eb15da_6
+prefix: /opt/conda/envs/upimapi