diff --git a/recipes/breseq/build.sh b/recipes/breseq/build.sh
index f1db83897d20e..86eed127a90af 100644
--- a/recipes/breseq/build.sh
+++ b/recipes/breseq/build.sh
@@ -1,5 +1,16 @@
 #!/bin/bash
+
 set -eux
-./configure --prefix=$PREFIX
-make -j ${CPU_COUNT}
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export M4="${BUILD_PREFIX}/bin/m4"
+
+autoreconf -if
+./configure --prefix="${PREFIX}" \
+	CXX="${CXX}" \
+	CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS}"
+make -j "${CPU_COUNT}"
 make install
diff --git a/recipes/breseq/meta.yaml b/recipes/breseq/meta.yaml
index 16e27485c1fd7..bc10a5dbbd9ac 100644
--- a/recipes/breseq/meta.yaml
+++ b/recipes/breseq/meta.yaml
@@ -9,19 +9,20 @@ source:
   sha256: "39b35e246ecd2b497c82a99765ca4d78a0400bc4a7518b7506b140229ccc0247"
 
 build:
-  number: 1
+  number: 2
   run_exports:
     - {{ pin_subpackage('breseq', max_pin="x.x") }}
 
 requirements:
   build:
     - make
-    - {{ compiler("c") }}
     - {{ compiler("cxx") }}
+    - autoconf
+    - automake
+    - libtool
   host:
     - zlib
   run:
-    - zlib
     - r-base
     - r-cairo
     - bowtie2 >=2.0.0,!=2.0.3,!=2.0.4,!=2.3.1
@@ -36,11 +37,17 @@ about:
   license: GPL-2.0-or-later
   license_family: GPL
   license_file: COPYING
-  summary: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
-    data.
+  summary: "A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
+    data."
   doc_url: "https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/"
+  dev_url: https://github.com/barricklab/breseq
 
 extra:
   additional-platforms:
     - linux-aarch64
     - osx-arm64
+  identifiers:
+    - biotools:breseq
+    - biotools:breseq_bam2aln
+    - biotools:breseq_bam2cov
+    - usegalaxy-eu:breseq