diff --git a/var/spack/repos/builtin/packages/py-checkm-genome/package.py b/var/spack/repos/builtin/packages/py-checkm-genome/package.py
index f544f92f2c..7d6d73d34e 100644
--- a/var/spack/repos/builtin/packages/py-checkm-genome/package.py
+++ b/var/spack/repos/builtin/packages/py-checkm-genome/package.py
@@ -13,18 +13,26 @@ class PyCheckmGenome(PythonPackage):
     homepage = "https://ecogenomics.github.io/CheckM"
     pypi = "checkm-genome/checkm-genome-1.0.11.tar.gz"
 
+    version("1.2.1", sha256="33907aa7bbf029f8345e33df80d5c89b7a719041f55ece4f7470cd061c8eff76")
     version("1.0.13", sha256="ffb7e4966c0fac07c7e6e7db6f6eb5b48587fa83987f8a68efbaff2afb7da82e")
     version("1.0.11", sha256="e475d9817d12fa771dbccc80f47758b742fc67c25261dc8ca0c0dc898c2a5190")
 
     # pip silently replaces distutils with setuptools
-    depends_on("py-setuptools", type="build")
+
+    depends_on("python@2.7.0:2.7", type=("build", "run"), when="@:1.0.18")
+    depends_on("python@3:", type=("build", "run"), when="@1.1.0:")
+    depends_on("py-setuptools", type=("build", "run"))
     depends_on("hmmer@3.1b1:", type=("build", "run"))
     depends_on("pplacer", type=("build", "run"))
     depends_on("prodigal@2.6.1:", type=("build", "run"))
-    depends_on("python@2.7.0:2.7", type=("build", "run"))
     depends_on("py-backports-functools-lru-cache", type=("build", "run"), when="^python@:3.2")
-    depends_on("py-numpy@1.8.0:", type=("build", "run"))
-    depends_on("py-scipy@0.9.0:", type=("build", "run"))
-    depends_on("py-matplotlib@1.3.1:2.2.3", type=("build", "run"))
-    depends_on("py-pysam@0.8.3:", type=("build", "run"))
-    depends_on("py-dendropy@4.0.0:", type=("build", "run"))
+    depends_on("py-numpy@1.8.0:", type=("build", "run"), when="@0.9.5:1.0.18")
+    depends_on("py-numpy@1.21.3:", type=("build", "run"), when="@1.2.0:")
+    depends_on("py-scipy@0.9.0:", type=("build", "run"), when="@0.9.5:1.0.18")
+    depends_on("py-scipy@1.7.3:", type=("build", "run"), when="@1.2.0")
+    depends_on("py-matplotlib@1.3.1:", type=("build", "run"), when="@0.9.5:1.0.18")
+    depends_on("py-matplotlib@3.5.1:", type=("build", "run"), when="@1.2.0:")
+    depends_on("py-pysam@0.8.3:", type=("build", "run"), when="@1.0.5:1.0.18")
+    depends_on("py-pysam@0.19.0:", type=("build", "run"), when="@1.2.0:")
+    depends_on("py-dendropy@4.0.0:", type=("build", "run"), when="@1.0.0:1.0.18")
+    depends_on("py-dendropy@4.5.2:", type=("build", "run"), when="@1.2.0:")
diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py
index 4b91d188a3..f2df9eb37a 100644
--- a/var/spack/repos/builtin/packages/py-pysam/package.py
+++ b/var/spack/repos/builtin/packages/py-pysam/package.py
@@ -13,6 +13,7 @@ class PyPysam(PythonPackage):
     homepage = "https://github.com/pysam-developers/pysam"
     pypi = "pysam/pysam-0.14.1.tar.gz"
 
+    version("0.19.1", sha256="dee403cbdf232170c1e11cc24c76e7dd748fc672ad38eb0414f3b9d569b1448f")
     version("0.18.0", sha256="1d6d49a0b3c626fae410a93d4c80583a8b5ddaacc9b46a080b250dbcebd30a59")
     version("0.15.3", sha256="a98dd0a164aa664b1ab30a36f653752f00e93c13deeb66868597f4b2a30f7265")
     version("0.15.2", sha256="d049efd91ed5b1af515aa30280bc9cb46a92ddd15d546c9b21ee68a6ed4055d9")