From d945bd54215aa06a111f7a10cd9b262bb7d75212 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Thu, 24 Oct 2024 23:28:57 +0200 Subject: [PATCH 01/27] Committer: Anupam Gautam TIPP_plastid is a User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data --- recipes/tipp/build.sh | 92 ++++++++++++++++++++++++++++++++++++++++++ recipes/tipp/meta.yaml | 53 ++++++++++++++++++++++++ 2 files changed, 145 insertions(+) create mode 100644 recipes/tipp/build.sh create mode 100644 recipes/tipp/meta.yaml diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh new file mode 100644 index 0000000000000..3e821f1ebe988 --- /dev/null +++ b/recipes/tipp/build.sh @@ -0,0 +1,92 @@ +#!/bin/bash + +# Exit on any error +set -e + +# Initialize and update all submodules +git submodule update --init + +# Define variables for directories +KMC_DIR="src/kmc3" + +# Unset Conda-specific environment variables during KMC build +OLD_PREFIX=$PREFIX +unset PREFIX +unset CONDA_PREFIX + +# Enter the KMC directory, initialize and update its submodule +cd "$KMC_DIR" +git submodule update --init + +# Explicitly build Cloudflare's zlib to ensure it's used in KMC build +cd 3rd_party/cloudflare +./configure +make libz.a + +# Go back to KMC directory +cd ../.. + +# Set flags to use Cloudflare zlib +CFLAGS="-I$(pwd)/3rd_party/cloudflare" +LDFLAGS="-L$(pwd)/3rd_party/cloudflare" +export CFLAGS LDFLAGS + +# Build KMC with the correct zlib +make + +# Unset the flags after the KMC build to prevent issues later +unset CFLAGS +unset LDFLAGS + +# Restore the environment variables +export PREFIX=$OLD_PREFIX +export CONDA_PREFIX=$OLD_PREFIX + +# Go back to the src directory +cd ../.. + +# Build seqtk +SEQTK_DIR="src/seqtk" +cd "$SEQTK_DIR" +make + +# Go back to the src directory +cd .. +echo "we crossed this 1" +# Compile the readskmercount program, ensuring paths to KMC +#g++ -v -o readskmercount -I./kmc3 -L./kmc3/bin -lkmc_core -pthread + +# Compile readskmercount as an object first if it doesn't have a main +g++ -c readskmercount.opt.cpp -I./kmc3 + +echo "we crossed this 2" +# Then link it to create the executable +g++ -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread + + +echo "Installation completed successfully." + + +#CURRENT_PATH=$(pwd)/src +#export PATH=$CURRENT_PATH:$PATH +#export PATH=$CURRENT_PATH/seqtk:$PATH +# Copy everything to the Conda environments bin directory to ensure they're accessible +echo "Copying binaries to PREFIX..." +cp -r * $PREFIX/bin/ || { echo "Failed to copy binaries to PREFIX"; exit 1; } + +echo "Installation completed successfully." +echo "Copying activation and deactivation scripts..." +mkdir -p $PREFIX/etc/conda/activate.d +mkdir -p $PREFIX/etc/conda/deactivate.d + + + +echo 'export CURRENT_PATH=$CONDA_PREFIX/bin' >$PREFIX/etc/conda/activate.d/tipp.sh + +# Add TIPP and related tools to the PATH +echo 'export PATH=$CURRENT_PATH:$PATH' >> $PREFIX/etc/conda/activate.d/tipp.sh +echo 'export PATH=$CURRENT_PATH/seqtk:$PATH' >> $PREFIX/etc/conda/activate.d/tipp.sh +echo 'export PATH=$CURRENT_PATH/kmc3/bin:$PATH' >> $PREFIX/etc/conda/activate.d/tipp.sh + + +echo 'export PATH=$(echo $PATH | sed -e "s|$CONDA_PREFIX/bin:||g")' >$PREFIX/etc/conda/deactivate.d/tipp.sh diff --git a/recipes/tipp/meta.yaml b/recipes/tipp/meta.yaml new file mode 100644 index 0000000000000..fbb36307c0480 --- /dev/null +++ b/recipes/tipp/meta.yaml @@ -0,0 +1,53 @@ +package: + name: tipp + version: "1.1.0" + +source: + git_url: https://github.com/Wenfei-Xian/TIPP.git + git_tag: main # Use a specific release tag if necessary + +build: + number: 0 + #script: bash ./build.sh + +requirements: + build: + - gxx_linux-64 # For compiling C++ code + - python=3.7 + - make + - git + #- bioconductor-biostrings=2.68.1 # from bioconda + #- flye # from bioconda + #- graphaligner=1.0.17 # from bioconda + #- mcl=22.282 # from bioconda + #- minimap2=2.26 # from bioconda + #- spoa=4.1.4 # from bioconda + #- trf=4.09.1 # from bioconda + #- r-pheatmap=1.0.12 # from bioconda + #- r-igraph=1.5.1 # from conda-forge + #- r-stringdist=0.9.10 # from conda-forge + #- r-ggplot2=3.4.4 # from conda-forge + #- kmc=3.2.4 + - zlib=1.2.13 + - bzip2=1.0.8 + #- tiara # from pypi (requires pip install) + run: + - python=3.7 + - tiara + - graphaligner=1.0.17 + - flye + - minimap2=2.26 + - spoa=4.1.4 + - mcl=22.282 + - r-pheatmap=1.0.12 + - r-igraph=1.5.1 + - bioconductor-biostrings=2.68.1 + - r-stringdist=0.9.10 + - r-ggplot2=3.4.4 + - trf=4.09.1 + #- kmc + +about: + home: https://github.com/Wenfei-Xian/TIPP + license: MIT + summary: "TIPP: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data" From 4ab01ae028e6c8872a6dfc97126cadcaa2b2f1ab Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 15:08:09 +0200 Subject: [PATCH 02/27] Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov --- recipes/tipp/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh index 3e821f1ebe988..bd86b92837729 100644 --- a/recipes/tipp/build.sh +++ b/recipes/tipp/build.sh @@ -1,7 +1,7 @@ #!/bin/bash # Exit on any error -set -e +set -ex # Initialize and update all submodules git submodule update --init From 63b05b4af817350cf01e47c7a5f9d4d2fdc22865 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 15:13:24 +0200 Subject: [PATCH 03/27] Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov --- recipes/tipp/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh index bd86b92837729..7870f48d3c65d 100644 --- a/recipes/tipp/build.sh +++ b/recipes/tipp/build.sh @@ -32,7 +32,7 @@ LDFLAGS="-L$(pwd)/3rd_party/cloudflare" export CFLAGS LDFLAGS # Build KMC with the correct zlib -make +make -j"${CPU_COUNT}" # Unset the flags after the KMC build to prevent issues later unset CFLAGS From ec0b3c936aa1796b91188b39b7a0591d70898677 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 15:13:41 +0200 Subject: [PATCH 04/27] Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov --- recipes/tipp/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh index 7870f48d3c65d..b728e284be98c 100644 --- a/recipes/tipp/build.sh +++ b/recipes/tipp/build.sh @@ -48,7 +48,7 @@ cd ../.. # Build seqtk SEQTK_DIR="src/seqtk" cd "$SEQTK_DIR" -make +make -j"${CPU_COUNT}" # Go back to the src directory cd .. From 61cdfda095584ed26dc2b1371f824dc23680d23a Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 15:14:02 +0200 Subject: [PATCH 05/27] Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov --- recipes/tipp/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh index b728e284be98c..b4c7f1b0c259f 100644 --- a/recipes/tipp/build.sh +++ b/recipes/tipp/build.sh @@ -57,7 +57,7 @@ echo "we crossed this 1" #g++ -v -o readskmercount -I./kmc3 -L./kmc3/bin -lkmc_core -pthread # Compile readskmercount as an object first if it doesn't have a main -g++ -c readskmercount.opt.cpp -I./kmc3 +${CXX} -c readskmercount.opt.cpp -I./kmc3 echo "we crossed this 2" # Then link it to create the executable From 9ed0cdd0ec75bbfb57199d014dbb2dd437d03634 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 15:14:18 +0200 Subject: [PATCH 06/27] Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov --- recipes/tipp/build.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh index b4c7f1b0c259f..5a56ab62fd671 100644 --- a/recipes/tipp/build.sh +++ b/recipes/tipp/build.sh @@ -61,7 +61,7 @@ ${CXX} -c readskmercount.opt.cpp -I./kmc3 echo "we crossed this 2" # Then link it to create the executable -g++ -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread +${CXX} -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread echo "Installation completed successfully." From 2c0a077f187ff9e62234d3a10a3e218faa3f2649 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 15:14:30 +0200 Subject: [PATCH 07/27] Update recipes/tipp/meta.yaml Co-authored-by: Martin Grigorov --- recipes/tipp/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/tipp/meta.yaml b/recipes/tipp/meta.yaml index fbb36307c0480..ed86773903c42 100644 --- a/recipes/tipp/meta.yaml +++ b/recipes/tipp/meta.yaml @@ -12,7 +12,7 @@ build: requirements: build: - - gxx_linux-64 # For compiling C++ code + - {{ compiler('cxx') }} - python=3.7 - make - git From 01a006d7cde93eaf03937b6297325fab080e878a Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 15:23:36 +0200 Subject: [PATCH 08/27] Committer: Anupam Gautam suggestion incorporated --- recipes/tipp/build.sh | 45 ++++++++++++++++++++---------------------- recipes/tipp/meta.yaml | 23 ++------------------- 2 files changed, 23 insertions(+), 45 deletions(-) diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh index 5a56ab62fd671..0f4fb20b22bdf 100644 --- a/recipes/tipp/build.sh +++ b/recipes/tipp/build.sh @@ -4,7 +4,7 @@ set -ex # Initialize and update all submodules -git submodule update --init +#git submodule update --init # Define variables for directories KMC_DIR="src/kmc3" @@ -16,9 +16,9 @@ unset CONDA_PREFIX # Enter the KMC directory, initialize and update its submodule cd "$KMC_DIR" -git submodule update --init +#git submodule update --init -# Explicitly build Cloudflare's zlib to ensure it's used in KMC build +# Explicitly build Cloudflares zlib to ensure it's used in KMC build cd 3rd_party/cloudflare ./configure make libz.a @@ -32,7 +32,7 @@ LDFLAGS="-L$(pwd)/3rd_party/cloudflare" export CFLAGS LDFLAGS # Build KMC with the correct zlib -make -j"${CPU_COUNT}" +make -j "${CPU_COUNT}" # Unset the flags after the KMC build to prevent issues later unset CFLAGS @@ -48,30 +48,20 @@ cd ../.. # Build seqtk SEQTK_DIR="src/seqtk" cd "$SEQTK_DIR" -make -j"${CPU_COUNT}" +make -j "${CPU_COUNT}" # Go back to the src directory cd .. -echo "we crossed this 1" -# Compile the readskmercount program, ensuring paths to KMC -#g++ -v -o readskmercount -I./kmc3 -L./kmc3/bin -lkmc_core -pthread # Compile readskmercount as an object first if it doesn't have a main -${CXX} -c readskmercount.opt.cpp -I./kmc3 +${CXX} -c readskmercount.opt.cpp -I./kmc3 -echo "we crossed this 2" # Then link it to create the executable -${CXX} -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread +${CXX} -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread - -echo "Installation completed successfully." - - -#CURRENT_PATH=$(pwd)/src -#export PATH=$CURRENT_PATH:$PATH -#export PATH=$CURRENT_PATH/seqtk:$PATH # Copy everything to the Conda environments bin directory to ensure they're accessible echo "Copying binaries to PREFIX..." +mkdir -p $PREFIX/bin cp -r * $PREFIX/bin/ || { echo "Failed to copy binaries to PREFIX"; exit 1; } echo "Installation completed successfully." @@ -79,14 +69,21 @@ echo "Copying activation and deactivation scripts..." mkdir -p $PREFIX/etc/conda/activate.d mkdir -p $PREFIX/etc/conda/deactivate.d +# Add TIPP and related tools to the PATH - -echo 'export CURRENT_PATH=$CONDA_PREFIX/bin' >$PREFIX/etc/conda/activate.d/tipp.sh +cat << EOF > $PREFIX/etc/conda/activate.d/tipp.sh +# Set the current path to the conda environment's bin directory +export CURRENT_PATH=\$CONDA_PREFIX/bin # Add TIPP and related tools to the PATH -echo 'export PATH=$CURRENT_PATH:$PATH' >> $PREFIX/etc/conda/activate.d/tipp.sh -echo 'export PATH=$CURRENT_PATH/seqtk:$PATH' >> $PREFIX/etc/conda/activate.d/tipp.sh -echo 'export PATH=$CURRENT_PATH/kmc3/bin:$PATH' >> $PREFIX/etc/conda/activate.d/tipp.sh +export PATH=\$CURRENT_PATH:\$PATH +export PATH=\$CURRENT_PATH/seqtk:\$PATH +export PATH=\$CURRENT_PATH/kmc3/bin:\$PATH +EOF +cat << EOF > $PREFIX/etc/conda/deactivate.d/tipp.sh +# Remove the current conda environment's bin directory from PATH +export PATH=\$(echo \$PATH | sed -e "s|$CONDA_PREFIX/bin:||g") +EOF -echo 'export PATH=$(echo $PATH | sed -e "s|$CONDA_PREFIX/bin:||g")' >$PREFIX/etc/conda/deactivate.d/tipp.sh +echo "Installation completed successfully." diff --git a/recipes/tipp/meta.yaml b/recipes/tipp/meta.yaml index ed86773903c42..5b7277d3ccbdd 100644 --- a/recipes/tipp/meta.yaml +++ b/recipes/tipp/meta.yaml @@ -4,33 +4,15 @@ package: source: git_url: https://github.com/Wenfei-Xian/TIPP.git - git_tag: main # Use a specific release tag if necessary + git_tag: main build: number: 0 - #script: bash ./build.sh requirements: build: - - {{ compiler('cxx') }} + - {{ compiler('cxx') }} # For compiling C++ code - python=3.7 - - make - - git - #- bioconductor-biostrings=2.68.1 # from bioconda - #- flye # from bioconda - #- graphaligner=1.0.17 # from bioconda - #- mcl=22.282 # from bioconda - #- minimap2=2.26 # from bioconda - #- spoa=4.1.4 # from bioconda - #- trf=4.09.1 # from bioconda - #- r-pheatmap=1.0.12 # from bioconda - #- r-igraph=1.5.1 # from conda-forge - #- r-stringdist=0.9.10 # from conda-forge - #- r-ggplot2=3.4.4 # from conda-forge - #- kmc=3.2.4 - - zlib=1.2.13 - - bzip2=1.0.8 - #- tiara # from pypi (requires pip install) run: - python=3.7 - tiara @@ -45,7 +27,6 @@ requirements: - r-stringdist=0.9.10 - r-ggplot2=3.4.4 - trf=4.09.1 - #- kmc about: home: https://github.com/Wenfei-Xian/TIPP From 726f73bea3b89b2736c9ec26275f06aa0e096281 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 25 Oct 2024 18:10:41 +0200 Subject: [PATCH 09/27] Committer: Anupam Gautam updated meta and build. --- recipes/tipp/build.sh | 4 ---- recipes/tipp/meta.yaml | 4 +++- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh index 0f4fb20b22bdf..fa2fc82eba8d6 100644 --- a/recipes/tipp/build.sh +++ b/recipes/tipp/build.sh @@ -3,9 +3,6 @@ # Exit on any error set -ex -# Initialize and update all submodules -#git submodule update --init - # Define variables for directories KMC_DIR="src/kmc3" @@ -16,7 +13,6 @@ unset CONDA_PREFIX # Enter the KMC directory, initialize and update its submodule cd "$KMC_DIR" -#git submodule update --init # Explicitly build Cloudflares zlib to ensure it's used in KMC build cd 3rd_party/cloudflare diff --git a/recipes/tipp/meta.yaml b/recipes/tipp/meta.yaml index 5b7277d3ccbdd..ea660dfc40c57 100644 --- a/recipes/tipp/meta.yaml +++ b/recipes/tipp/meta.yaml @@ -4,7 +4,8 @@ package: source: git_url: https://github.com/Wenfei-Xian/TIPP.git - git_tag: main + git_tag: v1.1.0 + sha256: a3e57e709c206b742a954524b3f1d304d435e6f3cbe85617ade745b8ef5d5d7f build: number: 0 @@ -12,6 +13,7 @@ build: requirements: build: - {{ compiler('cxx') }} # For compiling C++ code + host: - python=3.7 run: - python=3.7 From 455eaf32755ad010ed530d4553dd00d51d6ac019 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 28 Oct 2024 16:44:18 +0100 Subject: [PATCH 10/27] GenEra conda recipes --- recipes/genera/build.sh | 30 ++++++++++++++++++++++++++++++ recipes/genera/meta.yaml | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 recipes/genera/build.sh create mode 100644 recipes/genera/meta.yaml diff --git a/recipes/genera/build.sh b/recipes/genera/build.sh new file mode 100644 index 0000000000000..07197bb3140ad --- /dev/null +++ b/recipes/genera/build.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +# Exit on any error +set -ex + +# Ensure all main scripts are executable +chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh + +# Clone the secondary repository and move the main script +git clone https://github.com/caraweisman/abSENSE.git +mv abSENSE/Run_abSENSE.py . +chmod +x Run_abSENSE.py + +# Define the Conda binary path +CONDABIN="${PREFIX}/bin" + +# Ensure the directory exists +mkdir -p "$CONDABIN" + + +# Move executables to the Conda binary directory +mv genEra "$CONDABIN" +mv Erassignment "$CONDABIN" +mv Run_abSENSE.py "$CONDABIN" +mv hmmEra "$CONDABIN" +mv tree2ncbitax "$CONDABIN" +mv FASTSTEP3R "$CONDABIN" +mv test_installation.sh "$CONDABIN" + +echo "Installation complete. Executables have been moved to ${CONDABIN}." diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml new file mode 100644 index 0000000000000..332ccf0f1d574 --- /dev/null +++ b/recipes/genera/meta.yaml @@ -0,0 +1,33 @@ +package: + name: genera + version: "1.4.2" + +source: + git_url: https://github.com/josuebarrera/GenEra.git + git_tag: v1.4.2 + sha256: d56c5f7430a33bf781a42b325c0cd813e862b06e14d486c411ba5909251ef206 + +build: + number: 0 + +requirements: + host: + - python=3.7.12 + run: + - python=3.7.12 + - diamond=2.1.10 + - mmseqs2=14.7e284 + - foldseek=3.915ef7d + - scipy=1.7.3 + - r-seqinr=4.2_16 + - r-optparse=1.7.3 + - r-bio3d=2.4_3 + - r-tidyverse=1.3.2 + - r-phytools=0.6_99 + - orthofinder=2.5.5 + - ncbitax2lin=2.3.2 + +about: + home: https://github.com/josuebarrera/GenEra.git + license: GPL-3.0 + summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra" From 7d2118012de3c9d6b6763a8b2ba00fdb946c63a8 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 28 Oct 2024 17:07:30 +0100 Subject: [PATCH 11/27] removed genera files --- recipes/genera/build.sh | 30 ------------------------------ recipes/genera/meta.yaml | 33 --------------------------------- 2 files changed, 63 deletions(-) delete mode 100644 recipes/genera/build.sh delete mode 100644 recipes/genera/meta.yaml diff --git a/recipes/genera/build.sh b/recipes/genera/build.sh deleted file mode 100644 index 07197bb3140ad..0000000000000 --- a/recipes/genera/build.sh +++ /dev/null @@ -1,30 +0,0 @@ -#!/bin/bash - -# Exit on any error -set -ex - -# Ensure all main scripts are executable -chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh - -# Clone the secondary repository and move the main script -git clone https://github.com/caraweisman/abSENSE.git -mv abSENSE/Run_abSENSE.py . -chmod +x Run_abSENSE.py - -# Define the Conda binary path -CONDABIN="${PREFIX}/bin" - -# Ensure the directory exists -mkdir -p "$CONDABIN" - - -# Move executables to the Conda binary directory -mv genEra "$CONDABIN" -mv Erassignment "$CONDABIN" -mv Run_abSENSE.py "$CONDABIN" -mv hmmEra "$CONDABIN" -mv tree2ncbitax "$CONDABIN" -mv FASTSTEP3R "$CONDABIN" -mv test_installation.sh "$CONDABIN" - -echo "Installation complete. Executables have been moved to ${CONDABIN}." diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml deleted file mode 100644 index 332ccf0f1d574..0000000000000 --- a/recipes/genera/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -package: - name: genera - version: "1.4.2" - -source: - git_url: https://github.com/josuebarrera/GenEra.git - git_tag: v1.4.2 - sha256: d56c5f7430a33bf781a42b325c0cd813e862b06e14d486c411ba5909251ef206 - -build: - number: 0 - -requirements: - host: - - python=3.7.12 - run: - - python=3.7.12 - - diamond=2.1.10 - - mmseqs2=14.7e284 - - foldseek=3.915ef7d - - scipy=1.7.3 - - r-seqinr=4.2_16 - - r-optparse=1.7.3 - - r-bio3d=2.4_3 - - r-tidyverse=1.3.2 - - r-phytools=0.6_99 - - orthofinder=2.5.5 - - ncbitax2lin=2.3.2 - -about: - home: https://github.com/josuebarrera/GenEra.git - license: GPL-3.0 - summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra" From 2e331f5364153d01401df29d980d22922957d6a4 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 28 Oct 2024 17:11:13 +0100 Subject: [PATCH 12/27] GenEra conda recipe --- recipes/genera/build.sh | 30 ++++++++++++++++++++++++++++++ recipes/genera/meta.yaml | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 recipes/genera/build.sh create mode 100644 recipes/genera/meta.yaml diff --git a/recipes/genera/build.sh b/recipes/genera/build.sh new file mode 100644 index 0000000000000..07197bb3140ad --- /dev/null +++ b/recipes/genera/build.sh @@ -0,0 +1,30 @@ +#!/bin/bash + +# Exit on any error +set -ex + +# Ensure all main scripts are executable +chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh + +# Clone the secondary repository and move the main script +git clone https://github.com/caraweisman/abSENSE.git +mv abSENSE/Run_abSENSE.py . +chmod +x Run_abSENSE.py + +# Define the Conda binary path +CONDABIN="${PREFIX}/bin" + +# Ensure the directory exists +mkdir -p "$CONDABIN" + + +# Move executables to the Conda binary directory +mv genEra "$CONDABIN" +mv Erassignment "$CONDABIN" +mv Run_abSENSE.py "$CONDABIN" +mv hmmEra "$CONDABIN" +mv tree2ncbitax "$CONDABIN" +mv FASTSTEP3R "$CONDABIN" +mv test_installation.sh "$CONDABIN" + +echo "Installation complete. Executables have been moved to ${CONDABIN}." diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml new file mode 100644 index 0000000000000..332ccf0f1d574 --- /dev/null +++ b/recipes/genera/meta.yaml @@ -0,0 +1,33 @@ +package: + name: genera + version: "1.4.2" + +source: + git_url: https://github.com/josuebarrera/GenEra.git + git_tag: v1.4.2 + sha256: d56c5f7430a33bf781a42b325c0cd813e862b06e14d486c411ba5909251ef206 + +build: + number: 0 + +requirements: + host: + - python=3.7.12 + run: + - python=3.7.12 + - diamond=2.1.10 + - mmseqs2=14.7e284 + - foldseek=3.915ef7d + - scipy=1.7.3 + - r-seqinr=4.2_16 + - r-optparse=1.7.3 + - r-bio3d=2.4_3 + - r-tidyverse=1.3.2 + - r-phytools=0.6_99 + - orthofinder=2.5.5 + - ncbitax2lin=2.3.2 + +about: + home: https://github.com/josuebarrera/GenEra.git + license: GPL-3.0 + summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra" From 1c55c53b584b2c7a370cd75c2db8b8d90f9f30bb Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 28 Oct 2024 17:17:38 +0100 Subject: [PATCH 13/27] cleaning --- recipes/tipp/build.sh | 85 ------------------------------------------ recipes/tipp/meta.yaml | 36 ------------------ 2 files changed, 121 deletions(-) delete mode 100644 recipes/tipp/build.sh delete mode 100644 recipes/tipp/meta.yaml diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh deleted file mode 100644 index fa2fc82eba8d6..0000000000000 --- a/recipes/tipp/build.sh +++ /dev/null @@ -1,85 +0,0 @@ -#!/bin/bash - -# Exit on any error -set -ex - -# Define variables for directories -KMC_DIR="src/kmc3" - -# Unset Conda-specific environment variables during KMC build -OLD_PREFIX=$PREFIX -unset PREFIX -unset CONDA_PREFIX - -# Enter the KMC directory, initialize and update its submodule -cd "$KMC_DIR" - -# Explicitly build Cloudflares zlib to ensure it's used in KMC build -cd 3rd_party/cloudflare -./configure -make libz.a - -# Go back to KMC directory -cd ../.. - -# Set flags to use Cloudflare zlib -CFLAGS="-I$(pwd)/3rd_party/cloudflare" -LDFLAGS="-L$(pwd)/3rd_party/cloudflare" -export CFLAGS LDFLAGS - -# Build KMC with the correct zlib -make -j "${CPU_COUNT}" - -# Unset the flags after the KMC build to prevent issues later -unset CFLAGS -unset LDFLAGS - -# Restore the environment variables -export PREFIX=$OLD_PREFIX -export CONDA_PREFIX=$OLD_PREFIX - -# Go back to the src directory -cd ../.. - -# Build seqtk -SEQTK_DIR="src/seqtk" -cd "$SEQTK_DIR" -make -j "${CPU_COUNT}" - -# Go back to the src directory -cd .. - -# Compile readskmercount as an object first if it doesn't have a main -${CXX} -c readskmercount.opt.cpp -I./kmc3 - -# Then link it to create the executable -${CXX} -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread - -# Copy everything to the Conda environments bin directory to ensure they're accessible -echo "Copying binaries to PREFIX..." -mkdir -p $PREFIX/bin -cp -r * $PREFIX/bin/ || { echo "Failed to copy binaries to PREFIX"; exit 1; } - -echo "Installation completed successfully." -echo "Copying activation and deactivation scripts..." -mkdir -p $PREFIX/etc/conda/activate.d -mkdir -p $PREFIX/etc/conda/deactivate.d - -# Add TIPP and related tools to the PATH - -cat << EOF > $PREFIX/etc/conda/activate.d/tipp.sh -# Set the current path to the conda environment's bin directory -export CURRENT_PATH=\$CONDA_PREFIX/bin - -# Add TIPP and related tools to the PATH -export PATH=\$CURRENT_PATH:\$PATH -export PATH=\$CURRENT_PATH/seqtk:\$PATH -export PATH=\$CURRENT_PATH/kmc3/bin:\$PATH -EOF - -cat << EOF > $PREFIX/etc/conda/deactivate.d/tipp.sh -# Remove the current conda environment's bin directory from PATH -export PATH=\$(echo \$PATH | sed -e "s|$CONDA_PREFIX/bin:||g") -EOF - -echo "Installation completed successfully." diff --git a/recipes/tipp/meta.yaml b/recipes/tipp/meta.yaml deleted file mode 100644 index ea660dfc40c57..0000000000000 --- a/recipes/tipp/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -package: - name: tipp - version: "1.1.0" - -source: - git_url: https://github.com/Wenfei-Xian/TIPP.git - git_tag: v1.1.0 - sha256: a3e57e709c206b742a954524b3f1d304d435e6f3cbe85617ade745b8ef5d5d7f - -build: - number: 0 - -requirements: - build: - - {{ compiler('cxx') }} # For compiling C++ code - host: - - python=3.7 - run: - - python=3.7 - - tiara - - graphaligner=1.0.17 - - flye - - minimap2=2.26 - - spoa=4.1.4 - - mcl=22.282 - - r-pheatmap=1.0.12 - - r-igraph=1.5.1 - - bioconductor-biostrings=2.68.1 - - r-stringdist=0.9.10 - - r-ggplot2=3.4.4 - - trf=4.09.1 - -about: - home: https://github.com/Wenfei-Xian/TIPP - license: MIT - summary: "TIPP: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data" From 579c149bdb7c910c5c0284cef68d95448b0a55d3 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 28 Oct 2024 22:49:47 +0100 Subject: [PATCH 14/27] update --- recipes/genera/meta.yaml | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 332ccf0f1d574..fae5d2a4a3a6b 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -3,29 +3,30 @@ package: version: "1.4.2" source: - git_url: https://github.com/josuebarrera/GenEra.git - git_tag: v1.4.2 - sha256: d56c5f7430a33bf781a42b325c0cd813e862b06e14d486c411ba5909251ef206 + url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v1.4.2.tar.gz + sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 build: number: 0 + run_exports: + - {{ pin_subpackage('genera', max_pin="x.x") }} requirements: host: - - python=3.7.12 + - python =3.7.12 run: - - python=3.7.12 - - diamond=2.1.10 - - mmseqs2=14.7e284 - - foldseek=3.915ef7d - - scipy=1.7.3 - - r-seqinr=4.2_16 - - r-optparse=1.7.3 - - r-bio3d=2.4_3 - - r-tidyverse=1.3.2 - - r-phytools=0.6_99 - - orthofinder=2.5.5 - - ncbitax2lin=2.3.2 + - python =3.7.12 + - diamond =2.1.10 + - mmseqs2 =14.7e284 + - foldseek =3.915ef7d + - scipy =1.7.3 + - r-seqinr =4.2_16 + - r-optparse =1.7.3 + - r-bio3d =2.4_3 + - r-tidyverse =1.3.2 + - r-phytools =0.6_99 + - orthofinder =2.5.5 + - ncbitax2lin =2.3.2 about: home: https://github.com/josuebarrera/GenEra.git From 0305a7c683d2b05762911a9f2cf5321afb940ca9 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Tue, 29 Oct 2024 17:07:07 +0100 Subject: [PATCH 15/27] python updated --- recipes/genera/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index fae5d2a4a3a6b..815b4d12b29ed 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -13,9 +13,9 @@ build: requirements: host: - - python =3.7.12 + - python =3.8.0 run: - - python =3.7.12 + - python =3.8.0 - diamond =2.1.10 - mmseqs2 =14.7e284 - foldseek =3.915ef7d From 81192f34f6e595413041b8349d40a6d36d3a8e68 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 1 Nov 2024 13:55:41 +0100 Subject: [PATCH 16/27] changes added --- recipes/genera/build.sh | 3 +-- recipes/genera/meta.yaml | 7 +++++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/genera/build.sh b/recipes/genera/build.sh index 07197bb3140ad..ca0129e29bd65 100644 --- a/recipes/genera/build.sh +++ b/recipes/genera/build.sh @@ -6,8 +6,7 @@ set -ex # Ensure all main scripts are executable chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh -# Clone the secondary repository and move the main script -git clone https://github.com/caraweisman/abSENSE.git +# Move the main Run_abSENSE.py script mv abSENSE/Run_abSENSE.py . chmod +x Run_abSENSE.py diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 815b4d12b29ed..a21c2cc0e4c3a 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -3,8 +3,11 @@ package: version: "1.4.2" source: - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v1.4.2.tar.gz - sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 + - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v1.4.2.tar.gz + sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 + - git_url: https://github.com/caraweisman/abSENSE.git + git_rev: 4cbac1aeb6f1c33eb33058f87497d029ce2c1c6a + folder: abSENSE build: number: 0 From 88db21bedd9b1edfdc40881f657307b229c06688 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 4 Nov 2024 12:04:43 +0100 Subject: [PATCH 17/27] added test and abSENSE release --- recipes/genera/build.sh | 3 ++- recipes/genera/meta.yaml | 11 ++++++++--- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/recipes/genera/build.sh b/recipes/genera/build.sh index ca0129e29bd65..dae10970f15b0 100644 --- a/recipes/genera/build.sh +++ b/recipes/genera/build.sh @@ -6,7 +6,8 @@ set -ex # Ensure all main scripts are executable chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh -# Move the main Run_abSENSE.py script +#Move the main Run_abSENSE.py script + mv abSENSE/Run_abSENSE.py . chmod +x Run_abSENSE.py diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index a21c2cc0e4c3a..8f2406237a060 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -5,8 +5,8 @@ package: source: - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v1.4.2.tar.gz sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 - - git_url: https://github.com/caraweisman/abSENSE.git - git_rev: 4cbac1aeb6f1c33eb33058f87497d029ce2c1c6a + - url: https://github.com/caraweisman/abSENSE/archive/refs/tags/v1.0.0.tar.gz + sha256: a99090c10a66afae1fbad38d79d228199e9fbdae5173e71ad5d84b4c958dda54 folder: abSENSE build: @@ -31,7 +31,12 @@ requirements: - orthofinder =2.5.5 - ncbitax2lin =2.3.2 +test: + commands: + - genEra -h 2>&1 > /dev/null + about: home: https://github.com/josuebarrera/GenEra.git - license: GPL-3.0 + license: "GPL-3.0" + license_family: GPL3 summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra" From 449f89216c2b5e6fe6e2f11bd33ab83919e774e6 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 4 Nov 2024 14:34:38 +0100 Subject: [PATCH 18/27] added test and abSENSE release --- recipes/genera/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 8f2406237a060..e9db7a1dc7aa0 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -36,7 +36,7 @@ test: - genEra -h 2>&1 > /dev/null about: - home: https://github.com/josuebarrera/GenEra.git + home: https://github.com/josuebarrera/GenEra license: "GPL-3.0" license_family: GPL3 summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra" From 7e87ce3cae8c49a4864aecd253eabcba0ed271d8 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Fri, 15 Nov 2024 16:34:04 +0100 Subject: [PATCH 19/27] update --- recipes/genera/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index e9db7a1dc7aa0..9ff4aa8e988c1 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -11,14 +11,15 @@ source: build: number: 0 + noarch: generic run_exports: - {{ pin_subpackage('genera', max_pin="x.x") }} requirements: host: - - python =3.8.0 + - python >=3.8,<3.9 run: - - python =3.8.0 + - python >=3.8,<3.9 - diamond =2.1.10 - mmseqs2 =14.7e284 - foldseek =3.915ef7d @@ -37,6 +38,6 @@ test: about: home: https://github.com/josuebarrera/GenEra - license: "GPL-3.0" + license: "GPL-3.0-or-later" license_family: GPL3 summary: "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra" From 43ab6b918701dcfebd6347f5629ab1270931ecf7 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Sun, 17 Nov 2024 00:17:21 +0100 Subject: [PATCH 20/27] update --- recipes/genera/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 9ff4aa8e988c1..d8b14425d0723 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -20,7 +20,7 @@ requirements: - python >=3.8,<3.9 run: - python >=3.8,<3.9 - - diamond =2.1.10 + - diamond >=2.1.10 - mmseqs2 =14.7e284 - foldseek =3.915ef7d - scipy =1.7.3 @@ -28,7 +28,7 @@ requirements: - r-optparse =1.7.3 - r-bio3d =2.4_3 - r-tidyverse =1.3.2 - - r-phytools =0.6_99 + - r-phytools >=0.6_99 - orthofinder =2.5.5 - ncbitax2lin =2.3.2 From c34e66e5136f3e0b8db64ddb153521554616a686 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 18 Nov 2024 12:56:22 +0100 Subject: [PATCH 21/27] Update recipes/genera/meta.yaml Co-authored-by: Mervin Fansler --- recipes/genera/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index d8b14425d0723..53303dd12c710 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -34,7 +34,7 @@ requirements: test: commands: - - genEra -h 2>&1 > /dev/null + - genEra -h about: home: https://github.com/josuebarrera/GenEra From 50c9c615e9fe8857d179a586440e2896b81e14e3 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 18 Nov 2024 12:56:36 +0100 Subject: [PATCH 22/27] Update recipes/genera/meta.yaml Co-authored-by: Mervin Fansler --- recipes/genera/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 53303dd12c710..8b1b19c0e28c2 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -1,9 +1,11 @@ +{% set version = '1.4.2' %} + package: - name: genera - version: "1.4.2" + name: genera + version: {{ version|replace('-', '_') }} source: - - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v1.4.2.tar.gz + - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v{{ version }}.tar.gz sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 - url: https://github.com/caraweisman/abSENSE/archive/refs/tags/v1.0.0.tar.gz sha256: a99090c10a66afae1fbad38d79d228199e9fbdae5173e71ad5d84b4c958dda54 From 4a1412aad9ad48575f7e3874ab615495381fe3c5 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 18 Nov 2024 12:58:19 +0100 Subject: [PATCH 23/27] Update meta.yaml --- recipes/genera/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 8b1b19c0e28c2..2ae46ec1b2cc1 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -37,6 +37,8 @@ requirements: test: commands: - genEra -h + - hmmEra -h + - test_installation.sh -h about: home: https://github.com/josuebarrera/GenEra From f4babdd317f5f0237a320429afac69c06bb55d6a Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 18 Nov 2024 18:36:20 +0100 Subject: [PATCH 24/27] Solved abSENSE License issue --- recipes/genera/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 2ae46ec1b2cc1..d21e4db4a7251 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -7,8 +7,8 @@ package: source: - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v{{ version }}.tar.gz sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 - - url: https://github.com/caraweisman/abSENSE/archive/refs/tags/v1.0.0.tar.gz - sha256: a99090c10a66afae1fbad38d79d228199e9fbdae5173e71ad5d84b4c958dda54 + - url: https://github.com/caraweisman/abSENSE/archive/refs/tags/v1.0.1.tar.gz + sha256: 853418e55c012c0dd409c97a70bbc9ecb69dfa7ccc94ec0f54d54ff99ec0e9f0 folder: abSENSE build: From e6c4d9c862bf91f88d78c34555c2f09d2c53a517 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 25 Nov 2024 10:15:30 +0100 Subject: [PATCH 25/27] resolved absense issue --- recipes/genera/build.sh | 6 ------ recipes/genera/meta.yaml | 5 ++--- 2 files changed, 2 insertions(+), 9 deletions(-) diff --git a/recipes/genera/build.sh b/recipes/genera/build.sh index dae10970f15b0..6703c9eb54fa6 100644 --- a/recipes/genera/build.sh +++ b/recipes/genera/build.sh @@ -6,11 +6,6 @@ set -ex # Ensure all main scripts are executable chmod +x genEra Erassignment hmmEra tree2ncbitax FASTSTEP3R test_installation.sh -#Move the main Run_abSENSE.py script - -mv abSENSE/Run_abSENSE.py . -chmod +x Run_abSENSE.py - # Define the Conda binary path CONDABIN="${PREFIX}/bin" @@ -21,7 +16,6 @@ mkdir -p "$CONDABIN" # Move executables to the Conda binary directory mv genEra "$CONDABIN" mv Erassignment "$CONDABIN" -mv Run_abSENSE.py "$CONDABIN" mv hmmEra "$CONDABIN" mv tree2ncbitax "$CONDABIN" mv FASTSTEP3R "$CONDABIN" diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index d21e4db4a7251..42493af0ec601 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -7,9 +7,6 @@ package: source: - url: https://github.com/josuebarrera/GenEra/archive/refs/tags/v{{ version }}.tar.gz sha256: acc49698b68151550b825c73f1f03dd268da2c73ecc7ac4c55eccb8bec5b1a54 - - url: https://github.com/caraweisman/abSENSE/archive/refs/tags/v1.0.1.tar.gz - sha256: 853418e55c012c0dd409c97a70bbc9ecb69dfa7ccc94ec0f54d54ff99ec0e9f0 - folder: abSENSE build: number: 0 @@ -33,12 +30,14 @@ requirements: - r-phytools >=0.6_99 - orthofinder =2.5.5 - ncbitax2lin =2.3.2 + - absense >=1.0.1 test: commands: - genEra -h - hmmEra -h - test_installation.sh -h + - Run_abSENSE.py -h about: home: https://github.com/josuebarrera/GenEra From c0d78b0121612e807f9f0d953e37a4200be283df Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 25 Nov 2024 11:12:52 +0100 Subject: [PATCH 26/27] Update recipes/genera/meta.yaml Co-authored-by: Mervin Fansler --- recipes/genera/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 42493af0ec601..8eda40a12c03f 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -37,7 +37,6 @@ test: - genEra -h - hmmEra -h - test_installation.sh -h - - Run_abSENSE.py -h about: home: https://github.com/josuebarrera/GenEra From 3182656000d228264aa69fc0e4c0bd2cfe2cc8c7 Mon Sep 17 00:00:00 2001 From: Anupam Gautam Date: Mon, 25 Nov 2024 11:17:48 +0100 Subject: [PATCH 27/27] Update meta.yaml --- recipes/genera/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/genera/meta.yaml b/recipes/genera/meta.yaml index 8eda40a12c03f..1937ba150929c 100644 --- a/recipes/genera/meta.yaml +++ b/recipes/genera/meta.yaml @@ -29,7 +29,7 @@ requirements: - r-tidyverse =1.3.2 - r-phytools >=0.6_99 - orthofinder =2.5.5 - - ncbitax2lin =2.3.2 + - ncbitax2lin >=2.3.2 - absense >=1.0.1 test: