Merge branch 'master' into add-pyskani

recipes/dysgu/build.sh

@@ -1,6 +1,13 @@
 #!/bin/bash
-export CFLAGS="-I$PREFIX/include"
-export LDFLAGS="-L$PREFIX/lib"
+export CFLAGS="${CFLAGS} -I${PREFIX}/include"
+export LDFLAGS="${LDFLAGS} -L{$PREFIX}/lib"
 export C_INCLUDE_PATH=${PREFIX}/include
 
+if [[ "$target_platform" == osx-64 ]]; then
+    SDKROOT=$(xcrun --sdk macosx --show-sdk-path)
+    echo "-isysroot is ${SDKROOT}"
+    export CFLAGS="${CFLAGS} -isysroot ${SDKROOT}"
+    export LDFLAGS="${LDFLAGS} -isysroot ${SDKROOT}"
+fi
+
 $PYTHON setup.py install --single-version-externally-managed --record=record.txt

recipes/dysgu/meta.yaml

@@ -11,8 +11,7 @@ source:
   sha256: {{ sha256hash }}
 
 build:
-  skip: true  # [osx and x86_64]
-  number: 0
+  number: 1
   binary_relocation: false
   entry_points:
     - dysgu = dysgu.main:cli

recipes/earlgrey/build.sh

@@ -6,24 +6,20 @@ set -x
 PACKAGE_HOME=${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}
 SCRIPT_DIR="${PACKAGE_HOME}/scripts/"
 
-
 # Create directories
 mkdir -p ${PREFIX}/bin
 mkdir -p ${PACKAGE_HOME}
 
-
 # Put package in share directory
 cp -rf * ${PACKAGE_HOME}/
 
-
 # Install SA-SSR (has to be done here because SA-SSR is an ancient repository without releases)
-git clone --depth 1 https://github.com/ridgelab/SA-SSR
+git clone --depth 1 https://github.com/TobyBaril/SA-SSR
 cd SA-SSR
 make
 cp -f bin/sa-ssr ${PREFIX}/bin/
 cd ../ && rm -rf SA-SSR/
 
-
 # Fixes to earlGrey executable
 sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGrey  #remove check that conda environment has a specific name
 sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGreyLibConstruct  #remove check that conda environment has a specific name
@@ -32,16 +28,13 @@ sed -i.bak "/CONDA_DEFAULT_ENV/,+4d" ${PACKAGE_HOME}/earlGreyAnnotationOnly  #re
 # Fixes sed command for executables so that it works on both linux and macos
 sed -i.bak "s|sed -i |sed -i.bak |g" ${PACKAGE_HOME}/earlGrey ${PACKAGE_HOME}/earlGreyLibConstruct ${PACKAGE_HOME}/earlGreyAnnotationOnly ${SCRIPT_DIR}/rcMergeRepeat* ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 
-
 # Remove -pa from RepeatClassifier
 sed -i.bak 's/RepeatClassifier -pa ${THREADS} /RepeatClassifier /' ${SCRIPT_DIR}/TEstrainer/TEstrainer
 
-
 # Remove -t parameter from sa-ssr (since multithreading doesn't work on OSX)
 sed -i.bak 's/-t ${THREADS} / /' ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 sed -i.bak 's/-t ${THREADS} / /' ${SCRIPT_DIR}/TEstrainer/TEstrainer
 
-
 # Add SCRIPT_DIR to correct path
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGrey
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${PACKAGE_HOME}/earlGreyLibConstruct
@@ -51,7 +44,6 @@ sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/headSwap.s
 sed -i.bak "s|SCRIPT_DIR=.*|SCRIPT_DIR=${SCRIPT_DIR}|g" ${SCRIPT_DIR}/autoPie.sh
 sed -i.bak "s|STRAIN_SCRIPTS=.*|STRAIN_SCRIPTS=${SCRIPT_DIR}/TEstrainer/scripts/|g" ${SCRIPT_DIR}/TEstrainer/TEstrainer_for_earlGrey.sh
 
-
 # Set permissions to files
 chmod +x ${PACKAGE_HOME}/earlGrey
 chmod +x ${PACKAGE_HOME}/earlGreyLibConstruct
@@ -77,7 +69,6 @@ echo "export PERL5LIB=${PREFIX}/share/RepeatMasker/:${PREFIX}/share/RepeatModele
 echo "#!/bin/sh" > "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivate.sh"
 echo "unset PERL5LIB" >> "${PREFIX}/etc/conda/deactivate.d/${PKG_NAME}_deactivate.sh"
 
-
 # Put earlGrey executable in bin
 cd ${PREFIX}/bin
 ln -sf ${PACKAGE_HOME}/earlGrey .

recipes/earlgrey/meta.yaml

@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 2
   skip: True # [osx]
   run_exports:
     - {{ pin_subpackage('earlgrey', max_pin='x') }}

recipes/mirscore/meta.yaml

@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('mirscore', max_pin="x.x") }}
 
@@ -27,6 +27,7 @@ requirements:
     - tqdm >=4.65
     - pandas >=2.0.0
     - cutadapt >=4.8
+    - strucvis >=0.8
 
 test:
   commands:

recipes/pytrf/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "pytrf" %}
-{% set version = "1.3.3" %}
-{% set sha256 = "f635dc817e0431d1f29dfda9ea2f2f901c89890443e15cd1f207975d6f84002f" %}
+{% set version = "1.4.1" %}
+{% set sha256 = "2329644eff32d5cf323e5333293cd68d8338c9574b1f76307dbc428ade85a96e" %}
 
 package:
   name: "{{ name|lower }}"

recipes/sc-musketeers/meta.yaml

@@ -0,0 +1,60 @@
+{% set name = "sc-musketeers" %}
+{% set version = "0.3.7" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/sc_musketeers-{{ version }}.tar.gz
+  sha256: e1480895be92b54762b09cb48886c9e68f5ec72e7cf8e48d938c22ada26ca94a
+
+build:
+  entry_points:
+    - sc-musketeers = scmusketeers:__main__.main_entry_point
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('sc-musketeers', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.10,<4.0
+    - poetry-core
+    - pip
+  run:
+    - python >=3.10.0,<4.0.0
+    - poetry >=1.8.1,<2.0.0
+    - numpy >=1.23.0,<2.0.0
+    - pytorch >=2.3.1,<3.0.0
+    - keras >=3.3.3,<4.0.0
+    - scanpy >=1.10.1,<2.0.0
+    - ax-platform >=0.4.0,<0.5.0
+    - neptune >=1.10.4,<2.0.0
+    - pympler >=1.0.1,<2.0.0
+    - tensorflow >=2.10.0,<3.0.0
+    - pillow >=11.0.0,<12.0.0
+    - matplotlib-base >=3.9.3,<4.0.0
+    - pandas >=2.2.3,<3.0.0
+    - scikit-learn >=1.5.2,<2.0.0
+    - seaborn >=0.13.2,<0.14.0
+
+test:
+  imports:
+    - scmusketeers
+  commands:
+    - pip check
+    - sc-musketeers --help
+  requires:
+    - pip
+
+about:
+  home: https://sc-musketeers.readthedocs.io/
+  summary: A tri-partite modular autoencoder for addressing imbalanced cell type annotation and batch effect reduction
+  license: GPL-3.0
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - becavin-lab

recipes/scib/meta.yaml

@@ -1,20 +1,20 @@
 {% set name = "scib" %}
-{% set version = "1.1.5" %}
+{% set version = "1.1.6" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 build:
-  number: 1
+  number: 0
   script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
   skip: True  # [ py < 38 or py > 311]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/scib-{{ version }}.tar.gz
-  sha256: 7ab3183065f2d861b64f88823a55cec767327a37ad6d0eaccce7b43c996293ad
+  sha256: 32faddc0bdfbd43eb50b7e6a5136cccc9a57585a7914070396373601a7b61adc
   patches:
     - setup_compiler.patch
 

recipes/tipp/build.sh

@@ -39,8 +39,14 @@ mkdir -p $PREFIX/bin/seqtk
 for file in *.pl; do
   sed -i.bak '1 s|^#!/usr/bin/perl$|#!/usr/bin/env perl|' "$file"
 done
+sed -i.bak '1i #!/usr/bin/env perl' html2repeatbed.pl
 
-cp graph.plot.r readskmercount TIPP.pl TIPP_polish.pl html2repeatbed.pl MSA.plot.r TIPP_plastid.pl TIPP_telomere_backup.pl readskmercount.cpp telomeres.visulization.r TIPP_plastid.v2.1.pl TIPP_telomere.pl "$PREFIX/bin/" || { echo "Failed to copy specific binaries to PREFIX"; exit 1; }
+for file in *.r; do
+  sed -i.bak '1i#!/usr/bin/env Rscript' "$file"
+done
+
+
+cp graph.plot.r readskmercount TIPP.pl TIPP_polish.pl html2repeatbed.pl MSA.plot.r TIPP_plastid.pl TIPP_telomere_backup.pl readskmercount.cpp telomeres.visulization.r TIPP_plastid.v2.1.pl TIPP_telomere.pl TIPPo.v2.3.pl TIPPo.v2.2.pl "$PREFIX/bin/" || { echo "Failed to copy specific binaries to PREFIX"; exit 1; }
 cp -r kmc3/bin $PREFIX/bin/kmc3/
 cp seqtk/seqtk $PREFIX/bin/seqtk/
 

recipes/tipp/meta.yaml

@@ -1,11 +1,11 @@
 package:
   name: tipp
-  version: "1.1.0"
+  version: "1.2.0"
 
 source:
   git_url: https://github.com/Wenfei-Xian/TIPP.git
-  git_tag: v1.1.0
-  sha256: a3e57e709c206b742a954524b3f1d304d435e6f3cbe85617ade745b8ef5d5d7f
+  git_tag: v1.2.0
+  sha256: fd3004af512956ab8eba076e7fc19778cf8daca36a11c27a5fcce3991412108b
 
 build:
   number: 0
@@ -18,10 +18,12 @@ requirements:
     - {{ compiler('cxx') }}  # For compiling C++ code
     - make
     - kmc
+    - libzlib >=1.2.13,<1.3.0
   host:
     - python >=3.8,<3.9
     - zlib
     - perl
+    - libzlib >=1.2.13,<1.3.0
   run:
     - python >=3.8,<3.9
     - libxcrypt
@@ -39,16 +41,18 @@ requirements:
     - trf =4.09.1
     - zlib
     - perl
+
 test:
   commands:
     - TIPP_plastid.v2.1.pl -h
     - TIPP_telomere.pl -h
+    - TIPPo.v2.3.pl -h
 
 about:
   home: https://github.com/Wenfei-Xian/TIPP
   license: "GPL-3.0-or-later"
   license_family: GPL3
-  summary: "TIPP: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data"
+  summary: "TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data"
 
 extra:
   skip-lints: