diff options
| author | Rene Ladan <rene@FreeBSD.org> | 2025-06-02 17:02:45 +0000 |
|---|---|---|
| committer | Rene Ladan <rene@FreeBSD.org> | 2025-06-02 17:02:45 +0000 |
| commit | 12191baead8520b49266479d22c09dffef583ae9 (patch) | |
| tree | 32af7d1bdd0d86fd83b976473ca6ecded9d8065e | |
| parent | d1a26385cab601e2acbfc9514726429e3a0760ca (diff) | |
biology/checkm: Remove expired port
2025-06-01 biology/checkm: Depends on expired science/py-DendroPy
| -rw-r--r-- | MOVED | 1 | ||||
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/checkm/Makefile | 30 | ||||
| -rw-r--r-- | biology/checkm/distinfo | 3 | ||||
| -rw-r--r-- | biology/checkm/pkg-descr | 13 |
5 files changed, 1 insertions, 47 deletions
@@ -4459,3 +4459,4 @@ textproc/py-textract||2025-06-02|Has expired: Depends on expiring textproc/py-ex databases/py-fastapi-users-db-ormar||2025-06-02|Has expired: Depends on expiring www/py-fastapi-users www/py-fastapi-users||2025-06-02|Has expired: Depends on expired devel/py-makefun multimedia/ffsubsync||2025-06-02|Has expired: Depends on expired multimedia/py-ffmpeg-python +biology/checkm||2025-06-02|Has expired: Depends on expired science/py-DendroPy diff --git a/biology/Makefile b/biology/Makefile index ea85f35b064d..9f2f693fcfc5 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -37,7 +37,6 @@ SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta - SUBDIR += checkm SUBDIR += chip-seq SUBDIR += clustal-omega SUBDIR += clustalw diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile deleted file mode 100644 index cb7cc7108d4a..000000000000 --- a/biology/checkm/Makefile +++ /dev/null @@ -1,30 +0,0 @@ -PORTNAME= CheckM -DISTVERSIONPREFIX= v -DISTVERSION= 1.2.3 -PORTREVISION= 1 -CATEGORIES= biology python - -MAINTAINER= yuri@FreeBSD.org -COMMENT= Quality assessment tool for the microbial genomes -WWW= https://ecogenomics.github.io/CheckM/ - -LICENSE= GPLv3 -LICENSE_FILE= ${WRKSRC}/LICENSE - -DEPRECATED= Depends on expired science/py-DendroPy -EXPIRATION_DATE=2025-06-01 - -RUN_DEPENDS= ${PYNUMPY} \ - ${PYTHON_PKGNAMEPREFIX}DendroPy>0:science/py-DendroPy@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \ - ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} - -USES= dos2unix python -USE_GITHUB= yes -GH_ACCOUNT= Ecogenomics -USE_PYTHON= distutils noflavors autoplist - -NO_ARCH= yes - -.include <bsd.port.mk> diff --git a/biology/checkm/distinfo b/biology/checkm/distinfo deleted file mode 100644 index c1da8633ab00..000000000000 --- a/biology/checkm/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -TIMESTAMP = 1730733018 -SHA256 (Ecogenomics-CheckM-v1.2.3_GH0.tar.gz) = 5f8340e71d3256ba8cf407d27bdc7914d1aa86b14b2d63d1e32cceb325e5aa82 -SIZE (Ecogenomics-CheckM-v1.2.3_GH0.tar.gz) = 1017616 diff --git a/biology/checkm/pkg-descr b/biology/checkm/pkg-descr deleted file mode 100644 index 4238256d225a..000000000000 --- a/biology/checkm/pkg-descr +++ /dev/null @@ -1,13 +0,0 @@ -CheckM provides a set of tools for assessing the quality of genomes recovered -from isolates, single cells, or metagenomes. - -It provides robust estimates of genome completeness and contamination by using -collocated sets of genes that are ubiquitous and single-copy within a -phylogenetic lineage. - -Assessment of genome quality can also be examined using plots depicting key -genomic characteristics (e.g., GC, coding density) which highlight sequences -outside the expected distributions of a typical genome. CheckM also provides -tools for identifying genome bins that are likely candidates for merging based -on marker set compatibility, similarity in genomic characteristics, and -proximity within a reference genome tree. |