better conda packaging and fix concoct error

jtamames · Jul 11, 2023 · ba9a595 · ba9a595
1 parent f9e3891
commit ba9a595
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diff --git a/README.md b/README.md
@@ -53,7 +53,7 @@ SqueezeMeta is intended to be run in a x86-64 Linux OS (tested in Ubuntu and Cen
 
 and then use `mamba` to install SqueezeMeta
 
-`mamba create -n SqueezeMeta -c anaconda -c conda-forge -c bioconda -c fpusan squeezemeta=1.6 --no-channel-priority`
+`mamba create -n SqueezeMeta -c conda-forge -c bioconda -c anaconda -c fpusan  squeezemeta=1.6 --no-channel-priority`
 
 This will create a new conda environment named SqueezeMeta, which must then be activated.
 

diff --git a/VENDORED-TOOLS.md b/VENDORED-TOOLS.md
@@ -44,6 +44,7 @@ SqueezeMeta redistributes the following third-party software:
   - Add `-markerpath` as an additional command line argument
 * [MetaBAT](https://bitbucket.org/berkeleylab/metabat)
 * [CONCOCT](https://github.com/BinPro/CONCOCT)
+  - Fix an error in transform.py with newer version of scikit-kearn
 * [DAS tool](https://github.com/cmks/DAS_Tool)
   - Add extra logging, remove some superfluous error messages
   - Explicitly load `library(methods)` in DAS_Tool.R since Rscript does not load it on startup (even if R console does)

diff --git a/bin/CONCOCT-1.1.0/concoct/transform.py b/bin/CONCOCT-1.1.0/concoct/transform.py
@@ -2,6 +2,7 @@
 import pandas as p
 
 def perform_pca(d, nc, seed):
+    d.columns = d.columns.astype(str) # FPS; Fix error with newer version of scikit_learn
     pca_object = PCA(n_components=nc, random_state=seed).fit(d)
     return pca_object.transform(d), pca_object
 

diff --git a/conda/dev/meta.yaml b/conda/dev/meta.yaml
@@ -1,13 +1,14 @@
 package:
   name: squeezemeta-dev
-  version: '1.6.3beta1'
+  version: "1.6.2post2"
 
 source:
   git_url: https://github.com/jtamames/squeezemeta.git
-  git_tag: develop
+  git_tag: master
 
 requirements:
   build:
+    - python==3.10
     - r=3.6
     - r-ggplot2
     - r-reshape2
@@ -16,10 +17,9 @@ requirements:
     - bioconductor-pathview
     - perl=5.26
     - perl-app-cpanminus
-    - python=3.6
     - setuptools
     - cython >=0.19.1
-    - numpy
+    - numpy==1.25.0
     - scipy >=0.12.0
     - pandas >=0.11.0
     - biopython >=1.62b
@@ -31,42 +31,299 @@ requirements:
     - blas=*=mkl # To avoid openmp
     - readline=8
   run:
-    - python=3.6
-    - setuptools
+    # Packages originally specified in the template
+    - python==3.10.2
+    - setuptools==68.0.0
     - cython >=0.19.1
-    - {{ pin_compatible('numpy') }}
+    - numpy==1.25.0
     - scipy >=0.12.0
     - pandas >=0.11.0
     - biopython >=1.62b
     - scikit-learn >=0.18.0
     - nose >=1.3.0
-    - gsl
-    - openmp
+    - gsl==2.6
+    - openmp==8.0.1
     - samtools==1.11
-    - blas=*=mkl # To avoid openblas which causes trouble with CONCOCT
-    - future
-    - matplotlib
-    - dendropy
-    - pysam==0.20
-    - biopython
-    - perl=5.26
-    - perl-tie-ixhash
-    - perl-dbd-mysql
-    - perl-dbd-sqlite
-    - perl-lwp-simple
-    - perl-xml-libxml
-    - perl-xml-parser
-    - openjdk
-    - ruby=2.5
-    - r=3.6
-    - r-ggplot2
-    - r-reshape2
+    - blas==1.0
+    - future==0.18.3
+    - matplotlib==3.7.2
+    - dendropy==4.6.1
+    - pysam==0.20.0
+    - biopython==1.81
+    - perl==5.26.2
+    - perl-tie-ixhash==1.23
+    - perl-dbd-mysql==4.046
+    - perl-dbd-sqlite==1.64
+    - perl-lwp-simple==6.15
+    - perl-xml-libxml==2.0132
+    - perl-xml-parser==2.44_01
+    - openjdk==11.0.9.1
+    - ruby==2.5.7
+    - r==3.6
+    - r-ggplot2==3.3.3
+    - r-reshape2==1.4.4
     - r-doMC
-    - r-data.table
-    - bioconductor-pathview
-    - tree
-    - readline=8
-    - krona
+    - r-data.table==1.14.0
+    - bioconductor-pathview==1.26.0
+    - tree==2.1.1
+    - readline==8.1
+    - krona==2.8.1
+    # Extra dependencies
+    - bioconductor-annotationdbi==1.48.0
+    - bioconductor-biobase==2.46.0
+    - bioconductor-biocgenerics==0.32.0
+    - bioconductor-biostrings==2.54.0
+    - bioconductor-graph==1.64.0
+    - bioconductor-iranges==2.20.0
+    - bioconductor-kegggraph==1.46.0
+    - bioconductor-keggrest==1.26.0
+    - bioconductor-org.hs.eg.db==3.10.0
+    - bioconductor-rgraphviz==2.30.0
+    - bioconductor-s4vectors==0.24.0
+    - bioconductor-xvector==0.26.0
+    - bioconductor-zlibbioc==1.32.0
+    - brotli==1.0.9
+    - brotli-bin==1.0.9
+    - brotli-python==1.0.9
+    - bwidget==1.9.14
+    - cairo==1.16.0
+    - charset-normalizer==3.2.0
+    - contourpy==1.1.0
+    - cycler==0.11.0
+    - cython==0.29.36
+    - expat==2.5.0
+    - font-ttf-dejavu-sans-mono==2.37
+    - font-ttf-inconsolata==3.000
+    - font-ttf-source-code-pro==2.038
+    - font-ttf-ubuntu==0.83
+    - fontconfig==2.14.2
+    - fonts-conda-ecosystem==1
+    - fonts-conda-forge==1
+    - fonttools==4.40.0
+    - freetype==2.12.1
+    - fribidi==1.0.10
+    - gdbm==1.18
+    - gettext==0.21.1
+    - giflib==5.2.1
+    - gmp==6.2.1
+    - graphite2==1.3.13
+    - gst-plugins-base==1.18.5
+    - gstreamer==1.18.5
+    - gxx_impl_linux-64==9.5.0
+    - gxx_linux-64==9.5.0
+    - harfbuzz==2.9.1
+    - htslib==1.11
+    - idna==3.4
+    - intel-openmp==2022.1.0
+    - joblib==1.3.0
+    - jpeg==9e
+    - kernel-headers_linux-64==2.6.32
+    - keyutils==1.6.1
+    - kiwisolver==1.4.4
+    - lcms2==2.14
+    - ld_impl_linux-64==2.39
+    - libblas==3.9.0
+    - libbrotlicommon==1.0.9
+    - libbrotlidec==1.0.9
+    - libbrotlienc==1.0.9
+    - libcblas==3.9.0
+    - libclang==11.1.0
+    - libedit==3.1.20191231
+    - libev==4.33
+    - libevent==2.1.10
+    - libexpat==2.5.0
+    - libgcc-devel_linux-64==9.5.0
+    - libgcc-ng==13.1.0
+    - libgfortran-ng==13.1.0
+    - libgfortran5==13.1.0
+    - libglib==2.76.4
+    - libgomp==13.1.0
+    - libiconv==1.17
+    - liblapack==3.9.0
+    - libllvm11==11.1.0
+    - libnghttp2==1.51.0
+    - libnsl==2.0.0
+    - libogg==1.3.4
+    - libopus==1.3.1
+    - libpng==1.6.39
+    - libsanitizer==9.5.0
+    - libsqlite==3.42.0
+    - libssh2==1.10.0
+    - libstdcxx-devel_linux-64==9.5.0
+    - libstdcxx-ng==13.1.0
+    - libtiff==4.4.0
+    - libvorbis==1.3.7
+    - libwebp==1.2.4
+    - libwebp-base==1.2.4
+    - libzlib==1.2.13
+    - llvm-openmp==8.0.1
+    - make==4.3
+    - matplotlib-base==3.7.2
+    - mkl==2022.1.0
+    - munkres==1.1.4
+    - mysql-common==8.0.32
+    - mysql-connector-c==6.1.11
+    - mysql-libs==8.0.32
+    - ncurses==6.2
+    - nose==1.3.7
+    - nspr==4.35
+    - nss==3.89
+    - packaging==23.1
+    - pandas==2.0.3
+    - pango==1.48.10
+    - pcre==8.45
+    - pcre2==10.40
+    - perl-app-cpanminus==1.7044
+    - perl-carp==1.38
+    - perl-constant==1.33
+    - perl-dbi==1.642
+    - perl-encode==2.88
+    - perl-encode-locale==1.05
+    - perl-exporter==5.72
+    - perl-extutils-makemaker==7.36
+    - perl-file-path==2.16
+    - perl-file-temp==0.2304
+    - perl-parent==0.236
+    - perl-xml-namespacesupport==1.12
+    - perl-xml-sax==1.02
+    - perl-xml-sax-base==1.09
+    - pillow==9.3.0
+    - pip==23.1.2
+    - pixman==0.40.0
+    - platformdirs==3.8.1
+    - pooch==1.7.0
+    - pthread-stubs==0.4
+    - pyparsing==3.0.9
+    - pyqt==5.12.3
+    - pyqt-impl==5.12.3
+    - pyqt5-sip==4.19.18
+    - pyqtchart==5.12
+    - pyqtwebengine==5.12.1
+    - pysocks==1.7.1
+    - python-dateutil==2.8.2
+    - python-tzdata==2023.3
+    - pytz==2023.3
+    - qt==5.12.9
+    - r-askpass==1.1
+    - r-assertthat==0.2.1
+    - r-backports==1.2.1
+    - r-base==3.6.3
+    - r-bit==4.0.4
+    - r-bit64==4.0.5
+    - r-bitops==1.0_7
+    - r-blob==1.2.1
+    - r-boot==1.3_28
+    - r-brio==1.1.2
+    - r-cachem==1.0.5
+    - r-callr==3.7.0
+    - r-class==7.3_19
+    - r-cli==2.5.0
+    - r-cluster==2.1.2
+    - r-codetools==0.2_18
+    - r-colorspace==2.0_1
+    - r-crayon==1.4.1
+    - r-curl==4.3.1
+    - r-dbi==1.1.1
+    - r-desc==1.3.0
+    - r-diffobj==0.3.4
+    - r-digest==0.6.27
+    - r-domc==1.3.7
+    - r-ellipsis==0.3.2
+    - r-evaluate==0.14
+    - r-fansi==0.4.2
+    - r-farver==2.1.0
+    - r-fastmap==1.1.0
+    - r-foreach==1.5.1
+    - r-foreign==0.8_76
+    - r-glue==1.4.2
+    - r-gtable==0.3.0
+    - r-httr==1.4.2
+    - r-isoband==0.2.4
+    - r-iterators==1.0.13
+    - r-jsonlite==1.7.2
+    - r-kernsmooth==2.23_20
+    - r-labeling==0.4.2
+    - r-lattice==0.20_44
+    - r-lifecycle==1.0.0
+    - r-magrittr==2.0.1
+    - r-mass==7.3_54
+    - r-matrix==1.3_3
+    - r-memoise==2.0.0
+    - r-mgcv==1.8_35
+    - r-mime==0.10
+    - r-munsell==0.5.0
+    - r-nlme==3.1_152
+    - r-nnet==7.3_16
+    - r-openssl==1.4.4
+    - r-pillar==1.6.1
+    - r-pkgconfig==2.0.3
+    - r-pkgload==1.2.1
+    - r-plogr==0.2.0
+    - r-plyr==1.8.6
+    - r-png==0.1_7
+    - r-praise==1.0.0
+    - r-processx==3.5.2
+    - r-ps==1.6.0
+    - r-r6==2.5.0
+    - r-rcolorbrewer==1.1_2
+    - r-rcpp==1.0.6
+    - r-rcurl==1.98_1.3
+    - r-recommended==3.6
+    - r-rematch2==2.1.2
+    - r-rlang==0.4.11
+    - r-rpart==4.1_15
+    - r-rprojroot==2.0.2
+    - r-rsqlite==2.2.5
+    - r-rstudioapi==0.13
+    - r-scales==1.1.1
+    - r-spatial==7.3_14
+    - r-stringi==1.6.2
+    - r-stringr==1.4.0
+    - r-survival==3.2_11
+    - r-sys==3.4
+    - r-testthat==3.0.2
+    - r-tibble==3.1.2
+    - r-utf8==1.2.1
+    - r-vctrs==0.3.8
+    - r-viridislite==0.4.0
+    - r-waldo==0.2.5
+    - r-withr==2.4.2
+    - r-xml==3.99_0.3
+    - requests==2.31.0
+    - scikit-learn==1.3.0
+    - scipy==1.11.1
+    - sed==4.8
+    - six==1.16.0
+    - sqlite==3.37.0
+    - threadpoolctl==3.1.0
+    - tk==8.6.12
+    - tktable==2.10
+    - tornado==6.3.2
+    - typing-extensions==4.7.1
+    - typing_extensions==4.7.1
+    - tzdata==2023c
+    - unicodedata2==15.0.0
+    - urllib3==2.0.3
+    - wheel==0.40.0
+    - xorg-fixesproto==5.0
+    - xorg-inputproto==2.3.2
+    - xorg-kbproto==1.0.7
+    - xorg-libice==1.1.1
+    - xorg-libsm==1.2.4
+    - xorg-libx11==1.8.6
+    - xorg-libxau==1.0.11
+    - xorg-libxdmcp==1.1.3
+    - xorg-libxext==1.3.4
+    - xorg-libxfixes==5.0.3
+    - xorg-libxi==1.7.10
+    - xorg-libxrender==0.9.11
+    - xorg-libxtst==1.2.3
+    - xorg-recordproto==1.14.2
+    - xorg-renderproto==0.11.1
+    - xorg-xextproto==7.3.0
+    - xorg-xproto==7.0.31
+    - yaml==0.2.5
+    - zlib==1.2.13
 
 build:
   noarch: generic