From 197d365d40dcb3c57f17e11d18b96441cf5d68af Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Thu, 7 Nov 2024 18:42:29 -0600
Subject: [PATCH] biology/biostar-tools: Update to 2.0

Add ucsc-userapps to metaport.
It was previously excluded due to packaging restrictions.
---
 biology/biostar-tools/Makefile               |  8 +++++---
 biology/biostar-tools/distinfo               |  2 +-
 biology/biostar-tools/files/biostar-shell.in |  0
 biology/biostar-tools/files/pkg-message.in   | 13 +++++++++++++
 biology/biostar-tools/pkg-descr              |  7 ++-----
 biology/biostar-tools/pkg-message            | 11 -----------
 6 files changed, 21 insertions(+), 20 deletions(-)
 mode change 100755 => 100644 biology/biostar-tools/files/biostar-shell.in
 create mode 100644 biology/biostar-tools/files/pkg-message.in
 delete mode 100644 biology/biostar-tools/pkg-message

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
@@ -1,6 +1,7 @@
 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
@@ -63,7 +64,8 @@ RUN_DEPENDS=	wget>0:ftp/wget \
 		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
 
@@ -74,7 +76,7 @@ USES=		metaport python
 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:
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
@@ -1,8 +1,5 @@
 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
@@ -11,7 +8,7 @@ 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
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
-}
-]