clair3 advance

146_clair3/Clair3-remove_htslib.patch

@@ -0,0 +1,65 @@
+diff -ruN Clair3-1.0.4_orig/Makefile Clair3-1.0.4/Makefile
+--- Clair3-1.0.4_orig/Makefile	2023-09-07 14:28:29.842168186 +0100
++++ Clair3-1.0.4/Makefile	2023-09-07 14:35:52.320773700 +0100
+@@ -3,8 +3,10 @@
+
+ PYTHON ?= python3
+
+-all : libhts.a longphase libclair3.so
+-clean : clean_htslib clean_longphase clean_libclair3
++# all : libhts.a longphase libclair3.so
++# clean : clean_htslib clean_longphase clean_libclair3
++all : longphase libclair3.so
++clean : clean_longphase clean_libclair3
+
+ SAMVER	=	1.15.1
+ LPVER	=	1.3
+@@ -16,16 +18,16 @@
+ CPPFLAGS	=	-std=c++11 -Wall -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib
+ LP_CPPFLAGS	 =	-std=c++11 -Wall -g -O3 -I ${PREFIX}/include -L ${PREFIX}/lib -Wl,-rpath=${PREFIX}/lib
+
+-samtools-$(SAMVER)/Makefile:
+-		curl -L -o samtools-${SAMVER}.tar.bz2 https://github.com/samtools/samtools/releases/download/${SAMVER}/samtools-${SAMVER}.tar.bz2; \
+-		tar -xjf samtools-${SAMVER}.tar.bz2; \
+-		rm samtools-${SAMVER}.tar.bz2
+-
+-libhts.a: samtools-$(SAMVER)/Makefile
+-	# this is required only to add in -fpic so we can build python module
+-	@echo "\x1b[1;33mMaking $(@F)\x1b[0m"
+-	cd samtools-${SAMVER}/htslib-${SAMVER}; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
+-	cp samtools-${SAMVER}/htslib-${SAMVER}/$@ $@
++# samtools-$(SAMVER)/Makefile:
++# 		curl -L -o samtools-${SAMVER}.tar.bz2 https://github.com/samtools/samtools/releases/download/${SAMVER}/samtools-${SAMVER}.tar.bz2; \
++# 		tar -xjf samtools-${SAMVER}.tar.bz2; \
++# 		rm samtools-${SAMVER}.tar.bz2
++
++# libhts.a: samtools-$(SAMVER)/Makefile
++# 	# this is required only to add in -fpic so we can build python module
++# 	@echo "\x1b[1;33mMaking $(@F)\x1b[0m"
++# 	cd samtools-${SAMVER}/htslib-${SAMVER}; CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" ./configure; make CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
++# 	cp samtools-${SAMVER}/htslib-${SAMVER}/$@ $@
+
+
+ longphase-$(LPVER)/Makefile:
+@@ -39,15 +41,15 @@
+ 	cp longphase-${LPVER}/$@ $@
+
+
+-libclair3.so: samtools-${SAMVER}/htslib-${SAMVER}
++libclair3.so:
+ 	${PYTHON} build.py
+
+
+-.PHONY: clean_htslib
+-clean_htslib:
+-	cd samtools-${SAMVER} && make clean || exit 0
+-	cd samtools-${SAMVER}/htslib-${SAMVER} && make clean || exit 0
+-	rm libhts.a
++# .PHONY: clean_htslib
++# clean_htslib:
++# 	cd samtools-${SAMVER} && make clean || exit 0
++# 	cd samtools-${SAMVER}/htslib-${SAMVER} && make clean || exit 0
++# 	rm libhts.a
+
+ .PHONY: clean_longphase
+ clean_longphase:

146_clair3/cffi-1.15.1-GCCcore-11.3.0.eb

@@ -0,0 +1,38 @@
+easyblock = "PythonBundle"
+
+name = 'cffi'
+version = '1.15.1'
+
+homepage = 'https://cffi.readthedocs.io/en/latest/'
+description = """C Foreign Function Interface for Python. Interact with almost any C code from
+Python, based on C-like declarations that you can often copy-paste from header
+files or documentation.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+toolchainopts = {'pic': True}
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+]
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'use_pip': True,
+}
+
+exts_list = [
+    ('pycparser', '2.21', {
+        'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'],
+    }),
+    (name, version, {
+        'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'],
+    }),
+]
+
+moduleclass = 'tools'

146_clair3/clair3.eb

@@ -0,0 +1,46 @@
+easyblock = 'MakeCp'
+
+name = 'Clair3'
+version = '1.0.4'
+
+homepage = 'https://github.com/HKU-BAL/Clair3'
+description = """Clair3 is a germline small variant caller for long-reads.
+Clair3 makes the best of two major method categories: pileup calling handles
+most variant candidates with speed, and full-alignment tackles complicated candidates
+to maximize precision and recall. Clair3 runs fast and has superior performance,
+especially at lower coverage. Clair3 is simple and modular for easy deployment and
+integration."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+github_account = 'HKU-BAL'
+source_urls = [GITHUB_LOWER_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['Clair3-remove_htslib.patch']
+dependencies = [
+    ('Python', '3.10.4'),
+    ('mpath', '1.1.3'),
+    ('TensorFlow', '2.11.0'),
+    ('PyTables', '3.8.0'),
+    ('pigz', '2.7'),
+    ('cffi', '1.15.1'),
+    ('parallel', '20220722'),
+    ('SAMtools', '1.13'),
+    ('WhatsHap', '1.7'),
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('Automake', '1.16.5'),
+    ('cURL', '7.83.0'),
+    ('zstd', '1.5.2'),
+    ('HTSlib', '1.15.1'),
+]
+
+files_to_copy = [
+    (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf',
+      'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl',
+      'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC',
+      'misc/ibs'], 'bin'),
+    'doc',
+]
+
+moduleclass = 'bio'