diff --git a/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb new file mode 100644 index 00000000..b9a14fc1 --- /dev/null +++ b/236_NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'NGSpeciesID' +version = '0.3.0' + +homepage = 'https://github.com/ksahlin/NGSpeciesID' +description = "NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['71663ce280220d4e692cc6c3aea44f91e40b3143ed09a9462bdf2feb1d94aa9f'] + +dependencies = [ + ('Python', '3.11.3'), + ('python-parasail', '1.3.4'), + ('edlib', '1.2.7'), # TODO change version to python-1.3.9 + ('medaka', '1.11.3'), + ('spoa', '4.1.0'), + ('Racon', '1.5.0'), + ('minimap2', '2.26'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# no proper namespace for NGSpeciesID +options = {'modulename': 'modules.consensus'} + +# parasail requirements are too strict +preinstallopts = "sed -i 's/parasail==/parasail>=/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NGSpeciesID'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NGSpeciesID --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb index 8535acf8..9e0c95d8 100644 --- a/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb +++ b/236_NGSpeciesID/edlib-1.2.7-GCC-12.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'edlib' -version = '1.2.7' +version = '1.2.7' # TODO change version to python-1.3.9 homepage = 'https://martinsos.github.io/edlib' description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." diff --git a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb b/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb index 86267451..7defdab4 100644 --- a/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb +++ b/236_NGSpeciesID/medaka-1.11.3-foss-2023a.eb @@ -32,7 +32,7 @@ dependencies = [ ('minimap2', _minimap_ver), ('HTSlib', '1.18'), # for tabix, bgzip ('Racon', '1.5.0'), - ('edlib', '1.2.7'), + ('edlib', '1.2.7'), # TODO change version to python-1.3.9 ('pyspoa', '0.2.1'), ('python-parasail', '1.3.4'), ('ont-fast5-api', '4.1.2'), @@ -54,7 +54,8 @@ exts_list = [ (name, version, { 'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'], # Some requirements are too strict. - 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && ", + 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && " + + "sed -i 's/8, 9, 10/8, 9, 10, 11/g' setup.py && sed -i 's/,<3.11//g' setup.py && ", }), ]