diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile
index e96d678f6e63..ae9900e9a08b 100644
--- a/biology/sra-tools/Makefile
+++ b/biology/sra-tools/Makefile
@@ -1,65 +1,65 @@
 PORTNAME=	sra-tools
 DISTVERSION=	3.4.1
-PORTREVISION=	1
+PORTREVISION=	2
 CATEGORIES=	biology java
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	NCBI's toolkit for handling data in INSDC Sequence Read Archives
 WWW=		https://github.com/ncbi/sra-tools
 
 LICENSE=		PD LGPL21+
 LICENSE_COMB=		multi
 LICENSE_FILE_PD=	${WRKSRC}/LICENSE
 LICENSE_DISTFILES_LGPL21+ =
 
 ONLY_FOR_ARCHS=		aarch64 amd64
 ONLY_FOR_ARCHS_REASON=	Upstream explicitly supports specific platforms
 
 # hdf5 is dynamically loaded by some tools, but nothing links to it
 BUILD_DEPENDS=	bash:shells/bash
 RUN_DEPENDS=	hdf5>0:science/hdf5
 
 USES=		bison cmake java shebangfix
 USE_GITHUB=	yes
 USE_LDCONFIG=	${PREFIX}/lib64
 
 # Builds with earlier versions, but ngs-doc plist differs if jdk17 is present
 JAVA_VERSION=	17
 
 OPTIONS_DEFINE=	EXAMPLES
 
 SHEBANG_GLOB=	*.sh
 GH_ACCOUNT=	ncbi
 # FIXME: At the time this was added, sra-tools build required access to the
 # ncbi-vdb source tree.  Use a separate dependent port if that is no
 # longer the case.  CMakeLists.txt still looks for ../ncbi-vdb in 3.1.1.
 GH_TUPLE+=	ncbi:ncbi-vdb:${DISTVERSION}:vdb/ncbi-vdb
 
 CMAKE_ARGS+=	-DVDB_LIBDIR:STRING=${WRKSRC}/ncbi-vdb/build/lib
 # Prevent cmake from using a later Java version, if present
 CMAKE_ARGS+=	-DJAVA_HOME:PATH=${JAVA_HOME}
 
 PLIST_SUB=	PORTVERSION=${PORTVERSION}
 
 pre-configure:
 	# Reinplaces may follow static patches.  Run "make clean patch"
 	# before updating those patches so reinplaces do not get added to them.
 	@${REINPLACE_CMD} -e 's|"/etc/ncbi"|"${PREFIX}/etc/ncbi"|g' \
 		${WRKSRC}/ncbi-vdb/libs/kfg/config.c
 	@${REINPLACE_CMD} -e 's|/usr/local/bin|${PREFIX}/bin|g' \
 		${WRKSRC}/tools/external/driver-tool/file-path.posix.cpp
 	@${REINPLACE_CMD} -e 's|/../ncbi-vdb|/ncbi-vdb|g' \
 		${WRKSRC}/CMakeLists.txt
 	cd ${WRKSRC}/ncbi-vdb/build && cmake .. && make
 
 # FIXME: Unsure where the jquery version comes from and it differs on
 # amd64 (jquery-3.7.1.min.js) and aarch64 (jquery-3.6.1.min.js).
 # Just hack the version out for now.  Not sure we even need javadoc installed.
 post-stage:
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*.${DISTVERSION}
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib64/*.${DISTVERSION}
 
 post-stage-EXAMPLES-off:
 	${RM} -r ${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
diff --git a/biology/sra-tools/files/patch-build_env.cmake b/biology/sra-tools/files/patch-build_env.cmake
new file mode 100644
index 000000000000..b23966de6be0
--- /dev/null
+++ b/biology/sra-tools/files/patch-build_env.cmake
@@ -0,0 +1,13 @@
+--- build/env.cmake.orig	2026-05-12 21:39:17 UTC
++++ build/env.cmake
+@@ -470,8 +470,8 @@ if( Python3_EXECUTABLE )
+   find_package( Python3 COMPONENTS Interpreter Development )
+ # message(STATUS "Use: ${Python3_EXECUTABLE}")
+ 
+-  execute_process( COMMAND
+-         "${Python3_EXECUTABLE}" -m pip install --upgrade pip setuptools wheel )
++  # execute_process( COMMAND
++         # "${Python3_EXECUTABLE}" -m pip install --upgrade pip setuptools wheel )
+  endif()
+ endif()
+ 
diff --git a/biology/sra-tools/files/patch-build_install.sh b/biology/sra-tools/files/patch-build_install.sh
new file mode 100644
index 000000000000..aecbac2d7d62
--- /dev/null
+++ b/biology/sra-tools/files/patch-build_install.sh
@@ -0,0 +1,24 @@
+--- build/install.sh.orig	2026-05-12 20:23:33 UTC
++++ build/install.sh
+@@ -49,8 +49,12 @@ if [ "$EUID" -eq 0 ]; then
+         $SCRIPT_DIR/install-kfg.sh vdb-copy.kfg $SRC_DIR_COPY $KONFIG_DIR_ROOT $KFGSUMS_FILE
+     fi
+ 
+-PROFILE_FILE=/etc/profile.d/sra-tools
++    # We don't need these in FreeBSD ports, since the programs install
++    # into the default PATH and ldconfig points to the libraries.
++    if false; then
+ 
++    PROFILE_FILE=/etc/profile.d/sra-tools
++
+     echo "Updating ${PROFILE_FILE}.sh"
+     printf \
+ "#version ${VERSION}\n"\
+@@ -71,6 +75,7 @@ PROFILE_FILE=/etc/profile.d/sra-tools
+ "setenv NGS_LIBDIR ${LIBDIR}\n" \
+         >${PROFILE_FILE}.csh && chmod 644 ${PROFILE_FILE}.csh
+ 
++    endif
+ else
+ 
+     $SCRIPT_DIR/install-kfg.sh default.kfg  $SRC_DIR      $KONFIG_DIR $SRC_DIR/kfgsums
diff --git a/biology/sra-tools/files/patch-ngs_ngs-python_CMakeLists.txt b/biology/sra-tools/files/patch-ngs_ngs-python_CMakeLists.txt
new file mode 100644
index 000000000000..21bb29c991cd
--- /dev/null
+++ b/biology/sra-tools/files/patch-ngs_ngs-python_CMakeLists.txt
@@ -0,0 +1,19 @@
+--- ngs/ngs-python/CMakeLists.txt.orig	2026-03-25 20:33:21 UTC
++++ ngs/ngs-python/CMakeLists.txt
+@@ -29,11 +29,11 @@ if( Python3_EXECUTABLE )
+     #TODO: install
+ 
+     if( NOT LSB_RELEASE_ID_SHORT STREQUAL "Ubuntu" )
+-      add_test(
+-        NAME Test_NGS_Python_install
+-        COMMAND ${Python3_EXECUTABLE} -m pip install .
+-        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+-      )
++      # add_test(
++        # NAME Test_NGS_Python_install
++        # COMMAND ${Python3_EXECUTABLE} -m pip install .
++        # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
++      # )
+     else()
+       add_test(
+         NAME Test_NGS_Python_install