diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile
index ae02abc2c890..6002cae2fc71 100644
--- a/biology/biostar-tools/Makefile
+++ b/biology/biostar-tools/Makefile
@@ -1,84 +1,86 @@
 PORTNAME=	biostar-tools
-PORTVERSION=	1.11
+PORTVERSION=	2.0
 CATEGORIES=	biology python
+MASTER_SITES=	# empty
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	Meta-port for Biostar Handbook tools
 WWW=		https://www.biostarhandbook.com
 
 LICENSE=	BSD2CLAUSE
 
 # For a current list see http://data.biostarhandbook.com/install/conda.txt.
 # Also included are some programs not listed above, but mentioned in the text.
 # TODO: Add hdfview
 RUN_DEPENDS=	wget>0:ftp/wget \
 		curl>0:ftp/curl \
 		nano>0:editors/nano \
 		parallel>0:sysutils/parallel \
 		seqkit>0:biology/seqkit \
 		csvtk>0:science/csvtk \
 		${PYTHON_PKGNAMEPREFIX}csvkit>0:textproc/py-csvkit@${PY_FLAVOR} \
 		miller>0:textproc/miller \
 		ncbi-entrez-direct>0:biology/ncbi-entrez-direct \
 		readseq>0:biology/readseq \
 		snpeff>0:biology/snpeff \
 		picard-tools>0:biology/picard-tools \
 		bbmap>0:biology/bbmap \
 		minimap2>0:biology/minimap2 \
 		bwa>0:biology/bwa \
 		bowtie2>0:biology/bowtie2 \
 		samtools>0:biology/samtools \
 		emboss>0:biology/emboss \
 		bedtools>0:biology/bedtools \
 		bamtools>0:biology/bamtools \
 		${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \
 		seqtk>0:biology/seqtk \
 		datamash>0:textproc/datamash \
 		bcftools>0:biology/bcftools \
 		subread>0:biology/subread \
 		hisat2>0:biology/hisat2 \
 		trimmomatic>0:biology/trimmomatic \
 		fastqc>0:biology/fastqc \
 		picard-tools>0:biology/picard-tools \
 		ncbi-blast+>0:biology/ncbi-blast+ \
 		cd-hit>0:biology/cd-hit \
 		${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}pysam>0:biology/py-pysam@${PY_FLAVOR} \
 		freebayes>0:biology/freebayes \
 		p5-Net-SSLeay>0:security/p5-Net-SSLeay \
 		bioawk>0:biology/bioawk \
 		vt>0:biology/vt \
 		${PYTHON_PKGNAMEPREFIX}crossmap>0:biology/py-crossmap@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}goatools>0:biology/py-goatools@${PY_FLAVOR} \
 		erminej>0:biology/erminej \
 		${PYTHON_PKGNAMEPREFIX}ont-fast5-api>0:biology/py-ont-fast5-api@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}multiqc>0:biology/py-multiqc@${PY_FLAVOR} \
 		flash>0:biology/flash \
 		bfc:biology/bfc \
 		Jellyfish>0:biology/jellyfish \
 		mafft>0:biology/mafft \
 		clustal-omega>0:biology/clustal-omega \
 		sam2pairwise>0:biology/sam2pairwise \
 		kallisto>0:biology/kallisto \
 		bamutil>0:biology/bamutil \
 		${PYTHON_PKGNAMEPREFIX}deepTools>0:biology/py-deeptools@${PY_FLAVOR} \
 		igv>0:biology/igv \
-		gffread>0:biology/gffread
+		gffread>0:biology/gffread \
+		ucsc-userapps>0:biology/ucsc-userapps
 
 USES=		metaport python
 
 .include <bsd.port.pre.mk>
 
 # sra-tools is only supported on specific architectures
 .if ${ARCH} == amd64 || ${ARCH} == aarch64
 RUN_DEPENDS+=	sra-tools>0:biology/sra-tools
 .endif
 
-SUB_FILES=	biostar-shell
+SUB_FILES=	biostar-shell pkg-message
 PLIST_FILES=	bin/biostar-shell
 
 do-install:
 	@${MKDIR} ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_SCRIPT} ${WRKDIR}/biostar-shell ${STAGEDIR}${PREFIX}/bin
 
 .include <bsd.port.post.mk>
diff --git a/biology/biostar-tools/distinfo b/biology/biostar-tools/distinfo
index 19b785822b56..4bfd994ffd70 100644
--- a/biology/biostar-tools/distinfo
+++ b/biology/biostar-tools/distinfo
@@ -1 +1 @@
-TIMESTAMP = 1717414690
+TIMESTAMP = 1731026515
diff --git a/biology/biostar-tools/files/biostar-shell.in b/biology/biostar-tools/files/biostar-shell.in
old mode 100755
new mode 100644
diff --git a/biology/biostar-tools/files/pkg-message.in b/biology/biostar-tools/files/pkg-message.in
new file mode 100644
index 000000000000..5499288900c9
--- /dev/null
+++ b/biology/biostar-tools/files/pkg-message.in
@@ -0,0 +1,13 @@
+[
+{ type: install
+  message: <<EOM
+
+Biostar-tools installs all of the tools except emboss to the
+default PATH (normally /usr/local/bin) so they just work without any
+special environment.  Emboss commands are installed to
+%%PREFIX%%/emboss/bin due to conflicts with other packages.  Run
+"biostar-shell" to add the emboss commands to your PATH, and simply
+exit the shell to return your PATH to normal.
+EOM
+}
+]
diff --git a/biology/biostar-tools/pkg-descr b/biology/biostar-tools/pkg-descr
index 41a5f646b935..6cbffce10a0b 100644
--- a/biology/biostar-tools/pkg-descr
+++ b/biology/biostar-tools/pkg-descr
@@ -1,19 +1,16 @@
 Biostar-Tools is a metaport for installing all the tools necessary to
-work through the Biostar Handbook, except for bedGrapToBigWig, which
-has license restrictions.  If you need bedGraphToBigWig, run
-
-	cd /usr/ports/biology/ucsc-userapps && make install clean
+work through the Biostar Handbook.
 
 The handbook instructs the reader to install these tools mostly via
 bioconda, which then requires the user to activate the bioconda
 environment each time they want to use the tools.  You can also
 install conda packages on FreeBSD if you wish.  For details, see
 
 	/usr/ports/sysutils/linux-miniconda-installer/pkg-descr
 
-This meta-package installs all of the tools except emboss to the
+Biostar-tools installs all of the tools except emboss to the
 default PATH (normally /usr/local/bin) so they just work without any
 special environment.  Emboss commands are installed to
 /usr/local/emboss/bin due to conflicts with other packages.  Run
 "biostar-shell" to add the emboss commands to your PATH, and simply
 exit the shell to return your PATH to normal.
diff --git a/biology/biostar-tools/pkg-message b/biology/biostar-tools/pkg-message
deleted file mode 100644
index 4adbdc124805..000000000000
--- a/biology/biostar-tools/pkg-message
+++ /dev/null
@@ -1,11 +0,0 @@
-[
-{ type: install
-  message: <<EOM
-
-If you need bedGraphToBigWig, run:
-
-	cd ${PORTSDIR}/biology/ucsc-userapps && make install clean
-
-EOM
-}
-]