Merge branch 'master' into samtools

README.md

@@ -1,6 +1,8 @@
-# Eel recipes
+# Conda recipes arm64
 
-This project is a collection of [Conda](https://www.anaconda.com/products/distribution) recipes to build `aarch64` packages for common [**nf-core**](https://nf-co.re/) pipelines.
+This project is a collection of [Conda](https://docs.conda.io/en/latest/) recipes optimized for `arm64` CPU architecture, for tools mostly used by [**nf-core**](https://nf-co.re/) pipelines.
+
+Those recipes are made publicly available through [Seqera channel](https://anaconda.org/seqera) on Anaconda.org.
 
 ## Environment setup for building packages
 
@@ -25,7 +27,7 @@ conda config --system --add channels seqera
 
 5. Setup your SSH keys and clone this repo
 ```bash
-git clone [email protected]:seqeralabs/eel-recipes.git
+git clone [email protected]:seqeralabs/conda-recipes.git
 ```
 
 ## Build a package using conda build
@@ -38,6 +40,3 @@ cd recipes/pbzip2
 conda build .
 ```
 
-
-
-

recipes/bioconductor-biobase/meta.yaml

@@ -40,4 +40,3 @@ about:
 extra:
   identifiers:
     - biotools:biobase
-

recipes/bioconductor-dupradar/meta.yaml

@@ -1,4 +1,4 @@
-{% set version = "1.24.0" %}
+{% set version = "1.30.0" %}
 {% set name = "dupRadar" %}
 {% set bioc = "3.14" %}
 
@@ -10,7 +10,8 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: ce448594bfe36f7d2f96e35be3b56da8
+    - 'https://bioconductor.org/packages/release/bioc/src/contrib/dupRadar_1.30.0.tar.gz'
+  md5: 25020f4fc2033e3cb25d8fbc428219a6
 build:
   number: 0
   rpaths:

recipes/bioconductor-ebseq/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+mv DESCRIPTION DESCRIPTION.old
+grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
+$R CMD INSTALL --build .

recipes/bioconductor-ebseq/meta.yaml

@@ -0,0 +1,48 @@
+{% set version = "1.38.0" %}
+{% set name = "EBSeq" %}
+{% set bioc = "3.16" %}
+
+package:
+  name: 'bioconductor-{{ name|lower }}'
+  version: '{{ version }}'
+source:
+  url:
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
+    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
+    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
+  md5: 3dcbccf3dab22b82b2535991266b3f02
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  noarch: generic
+requirements:
+  host:
+    - 'r-base >=4.1,<4.2'
+    - r-blockmodeling
+    - r-gplots
+    - r-testthat
+  run:
+    - 'r-base >=4.1,<4.2'
+    - r-blockmodeling
+    - r-gplots
+    - r-testthat
+test:
+  commands:
+    - '$R -e "library(''{{ name }}'')"'
+about:
+  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
+  license: Artistic-2.0
+  summary: 'An R package for gene and isoform differential expression analysis of RNA-seq data'
+  description: 'Differential Expression analysis at both gene and isoform level using RNA-seq data'
+extra:
+  identifiers:
+    - biotools:ebseq
+    - doi:10.1093/bioinformatics/btt087
+  parent_recipe:
+    name: bioconductor-ebseq
+    path: recipes/bioconductor-ebseq
+    version: 1.20.0
+

recipes/bioconductor-iranges/meta.yaml

@@ -46,4 +46,3 @@ extra:
     name: bioconductor-iranges
     path: recipes/bioconductor-iranges
     version: 2.14.12
-

recipes/bioconductor-zlibbioc/meta.yaml

@@ -44,4 +44,3 @@ extra:
     name: bioconductor-zlibbioc
     path: recipes/bioconductor-zlibbioc
     version: 1.26.0
-

recipes/libpng/0001-Include-pkg-config-files-in-the-Windows-packages-too.patch

@@ -0,0 +1,29 @@
+--- libpng-1.6.38.orig/CMakeLists.txt	2022-09-14 16:42:00.000000000 -0300
++++ libpng-1.6.38/CMakeLists.txt	2022-09-15 10:09:48.728794541 -0300
+@@ -932,7 +932,7 @@
+ # We use the same files like ./configure, so we have to set its vars.
+ # Only do this on Windows for Cygwin - the files don't make much sense
+ # outside of a UNIX look-alike.
+-if(NOT WIN32 OR CYGWIN OR MINGW)
++if(1)
+   set(prefix      ${CMAKE_INSTALL_PREFIX})
+   set(exec_prefix ${CMAKE_INSTALL_PREFIX})
+   set(libdir      ${CMAKE_INSTALL_FULL_LIBDIR})
+@@ -1016,13 +1016,13 @@
+   install(FILES png.5
+           DESTINATION ${CMAKE_INSTALL_MANDIR}/man5)
+   # Install the pkg-config files.
++  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc
++          DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
++  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc
++          DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+   if(NOT CMAKE_HOST_WIN32 OR CYGWIN OR MINGW)
+-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc
+-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+     install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config
+             DESTINATION ${CMAKE_INSTALL_BINDIR})
+-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc
+-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
+     install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config
+             DESTINATION ${CMAKE_INSTALL_BINDIR})
+   endif()

recipes/libpng/0002-Ensure-that-lm-is-not-included-in-Windows-pkg-config.patch

@@ -0,0 +1,29 @@
+From ed4def04ed595c83ed8082845f5b807413b9400f Mon Sep 17 00:00:00 2001
+From: Mark Harfouche <[email protected]>
+Date: Wed, 6 Jul 2022 17:13:50 -0400
+Subject: [PATCH 2/2] Ensure that -lm is not included in Windows pkg-config
+
+---
+ CMakeLists.txt | 6 +++++-
+ 1 file changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 25e9e4d4e..649698ff6 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -825,7 +825,11 @@ if(1)
+   set(exec_prefix ${CMAKE_INSTALL_PREFIX})
+   set(libdir      ${CMAKE_INSTALL_FULL_LIBDIR})
+   set(includedir  ${CMAKE_INSTALL_FULL_INCLUDEDIR})
+-  set(LIBS        "-lz -lm")
++  if(NOT "${M_LIBRARY}" STREQUAL "")
++    set(LIBS        "-lz -lm")
++  else()
++    set(LIBS        "-lz")
++  endif()
+   configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng.pc.in
+     ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc @ONLY)
+   create_symlink(libpng.pc FILE ${PNGLIB_NAME}.pc)
+-- 
+2.34.1
+

recipes/libpng/bld.bat

@@ -0,0 +1,34 @@
+mkdir build-%SUBDIR%-%c_compiler%
+cd build-%SUBDIR%-%c_compiler%
+
+:: Configure.
+cmake -G Ninja                                  ^
+      -D CMAKE_INSTALL_PREFIX=%LIBRARY_PREFIX%  ^
+      -D ZLIB_LIBRARY=%LIBRARY_LIB%\zlib.lib    ^
+      -D ZLIB_INCLUDE_DIR=%LIBRARY_INC%         ^
+      -DCMAKE_C_FLAGS="%CFLAGS% -DWIN32"        ^
+      -DCMAKE_BUILD_TYPE=Release                ^
+      %SRC_DIR%
+if errorlevel 1 exit /b 1
+
+cmake --build . --target install
+if errorlevel 1 exit /b 1
+
+:: Test.
+ctest -C Release
+if errorlevel 1 exit 1
+
+:: Make copies of the .lib files without the embedded version number.
+copy %LIBRARY_LIB%\libpng16.lib %LIBRARY_LIB%\libpng.lib
+if errorlevel 1 exit 1
+
+copy %LIBRARY_LIB%\libpng16_static.lib %LIBRARY_LIB%\libpng_static.lib
+if errorlevel 1 exit 1
+
+:: Make copies of the .lib files without the 'lib' prefix.
+copy %LIBRARY_LIB%\libpng16.lib %LIBRARY_LIB%\png16.lib
+if errorlevel 1 exit 1
+
+copy %LIBRARY_LIB%\libpng16_static.lib %LIBRARY_LIB%\png16_static.lib
+if errorlevel 1 exit 1
+

recipes/libpng/build.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+# Get an updated config.sub and config.guess
+cp $BUILD_PREFIX/share/libtool/build-aux/config.* .
+
+export CFLAGS="$CFLAGS -I$PREFIX/include -L$PREFIX/lib"
+export CPPFLAGS="$CPPFLAGS -I$PREFIX/include"
+
+./configure --prefix=$PREFIX \
+            --with-zlib-prefix=$PREFIX
+
+make -j${CPU_COUNT} ${VERBOSE_AT}
+if [[ "${CONDA_BUILD_CROSS_COMPILATION}" != "1" ]]; then
+make check
+fi
+make install
+
+# We can remove this when we start using the new conda-build.
+find $PREFIX -name '*.la' -delete

recipes/libpng/conda_build_config.yaml

@@ -0,0 +1,37 @@
+BUILD: aarch64-conda_cos7-linux-gnu
+CI: azure
+c_compiler: gcc
+c_compiler_version: '10'
+cdt_arch: aarch64
+cdt_name: cos7
+channel_sources: conda-forge
+channel_targets: conda-forge main
+cpu_optimization_target: nocona
+cran_mirror: https://cran.r-project.org
+cxx_compiler: gxx
+docker_image: quay.io/condaforge/linux-anvil-aarch64
+extend_keys:
+- pin_run_as_build
+- ignore_version
+- ignore_build_only_deps
+- extend_keys
+fortran_compiler: gfortran
+ignore_build_only_deps:
+- numpy
+- python
+lua: '5'
+numpy: '1.16'
+perl: 5.26.2
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+  r-base:
+    min_pin: x.x
+    max_pin: x.x
+  zlib:
+    max_pin: x.x
+python: '3.9'
+r_base: '3.5'
+target_platform: linux-aarch64
+zlib: '1.2'

recipes/libpng/libpng-arm-free.patch

@@ -0,0 +1,16 @@
+index: libpng-1.6.36/pngread.c
+===================================================================
+--- libpng-1.6.36.orig/pngread.c	2018-12-01 15:36:00.000000000 +0100
++++ libpng-1.6.36/pngread.c	2019-01-28 12:41:14.044709070 +0100
+@@ -994,6 +994,11 @@ png_read_destroy(png_structrp png_ptr)
+    png_ptr->chunk_list = NULL;
+ #endif
+
++#if PNG_ARM_NEON_IMPLEMENTATION == 1
++   png_free(png_ptr, png_ptr->riffled_palette);
++   png_ptr->riffled_palette = NULL;
++#endif
++
+    /* NOTE: the 'setjmp' buffer may still be allocated and the memory and error
+     * callbacks are still set at this point.  They are required to complete the
+     * destruction of the png_struct itself.

recipes/libpng/meta.yaml

@@ -0,0 +1,77 @@
+# This file created by conda-build 3.22.0
+# meta.yaml template originally from:
+# /home/conda/recipe_root, last modified Fri Sep 16 16:57:13 2022
+# ------------------------------------------------
+
+package:
+  name: libpng
+  version: 1.6.38
+source:
+  patches:
+    - 0001-Include-pkg-config-files-in-the-Windows-packages-too.patch
+    - 0002-Ensure-that-lm-is-not-included-in-Windows-pkg-config.patch
+    - libpng-arm-free.patch
+  sha256: e2b5e1b4329650992c041996cf1269681b341191dc07ffed816c555769cceb77
+  url: http://download.sourceforge.net/libpng/libpng-1.6.38.tar.gz
+build:
+  number: '0'
+  run_exports:
+    - libpng >=1.6.38,<1.7.0a0
+  string: hf9034f9_0
+requirements:
+  build:
+    - _openmp_mutex 4.5 2_gnu
+    - autoconf 2.69 pl5321h689fa9f_11
+    - automake 1.16.5 pl5321h8af1aa0_0
+    - binutils_impl_linux-aarch64 2.36.1 h026399b_2
+    - binutils_linux-aarch64 2.36 h7854541_10
+    - gcc_impl_linux-aarch64 10.4.0 hbc23e19_16
+    - gcc_linux-aarch64 10.4.0 h72ad2ee_10
+    - kernel-headers_linux-aarch64 4.18.0 h5b4a56d_13
+    - ld_impl_linux-aarch64 2.36.1 h02ad14f_2
+    - libgcc-devel_linux-aarch64 10.4.0 hf691355_16
+    - libgcc-ng 12.1.0 h3242a24_16
+    - libgomp 12.1.0 h3242a24_16
+    - libnsl 2.0.0 hf897c2e_0
+    - libsanitizer 10.4.0 h69a60c7_16
+    - libstdcxx-ng 12.1.0 hd01590b_16
+    - libtool 2.4.6 h01db608_1008
+    - m4 1.4.18 h516909a_1001
+    - make 4.3 h309ac5b_1
+    - perl 5.32.1 2_hf897c2e_perl5
+    - sysroot_linux-aarch64 2.17 h43d7e78_13
+  host:
+    - _openmp_mutex 4.5 2_gnu
+    - libgcc-ng 12.1.0 h3242a24_16
+    - libgomp 12.1.0 h3242a24_16
+    - libzlib 1.2.12 h4e544f5_3
+    - zlib 1.2.12 h4e544f5_3
+  run:
+    - libgcc-ng >=12
+    - libzlib >=1.2.12,<1.3.0a0
+test:
+  commands:
+    - test -f ${PREFIX}/lib/libpng.a
+    - test -f ${PREFIX}/lib/libpng${SHLIB_EXT}
+    - libpng-config --version
+about:
+  description: 'libpng is the official PNG reference library. It supports almost all
+    PNG
+
+    features, is extensible, and has been extensively tested for over 20 years.
+
+    '
+  dev_url: https://sourceforge.net/p/libpng/code/ci/libpng16/tree/
+  doc_url: http://www.libpng.org/pub/png/libpng.html
+  home: http://www.libpng.org/pub/png/libpng.html
+  license: zlib-acknowledgement
+  license_file: LICENSE
+  license_url: http://www.libpng.org/pub/png/src/libpng-LICENSE.txt
+  summary: PNG reference library
+extra:
+  copy_test_source_files: true
+  final: true
+  recipe-maintainers:
+    - msarahan
+    - ocefpaf
+    - pkgw