fix: update sequenza

snappy_pipeline/workflows/somatic_targeted_seq_cnv_calling/Snakefile

@@ -241,11 +241,6 @@ rule somatic_targeted_seq_cnv_calling_cnvetti_off_target_postprocess:
 rule somatic_targeted_seq_cnv_calling_sequenza_install:
     output:
         **wf.get_output_files("sequenza", "install"),
-    params:
-        packages=[
-            {"name": "aroneklund/copynumber", "repo": "github"},
-            {"name": "sequenzatools/sequenza", "repo": "bitbucket"},
-        ],
     threads: wf.get_resource("sequenza", "install", "threads")
     resources:
         time=wf.get_resource("sequenza", "install", "time"),

snappy_wrappers/utils.py

@@ -2,8 +2,8 @@
 """Utility code for snappy_wrappers"""
 
 import os
-import re
 import subprocess
+import json
 
 __author__ = "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>"
 
@@ -57,67 +57,50 @@ def patched(*args, **kwargs):
     return patched
 
 
-def install_R_package(dest: str, name: str, repo: str):
-    """Installs R package <name> in directory <dest>
-
-    <repo> can be on of "cran", "bioconductor", "github", "bitbucket" or "local".
-
-    Github & bitbucket packages can be further defined in the <name>,
-    choosing a commit, a tag or a pull request (see the remotes package reference).
-    For local packages, the <name> must be the path to the package source.
-
-    In these cases, the routine tries to be clever and guess the package name from
-    the <name>. It implements the following recipes:
-
-    - basename of the path without (tar/zip) extension for local packages
-    - remove username, subdirectory and reference/release/pull request for github & bitbucket
-
-    When installation isn't successful, a subprocess.CalledProcessError is raised
-    """
-
-    assert repo in (
-        "cran",
-        "bioconductor",
-        "github",
-        "bitbucket",
-        "local",
-    ), f"Unknown/unimplemented repository {repo}"
-
+def install_R_package(
+    dest: str, name: str, repository: str = "cran", url: str | None = None
+) -> subprocess.CompletedProcess:
+    assert dest, "Missing R package destination folder"
     os.makedirs(os.path.dirname(dest), mode=0o750, exist_ok=True)
 
-    if repo == "cran":
-        install_cmd = f"install.packages('{name}', lib='{dest}', update=FALSE, ask=FALSE)"
-    elif repo == "bioconductor":
-        install_cmd = f"BiocManager::install('{name}', lib='{dest}', update=FALSE, ask=FALSE)"
-    elif repo == "github":
-        path = name
-        pattern = re.compile("^([^/]+)/([^/]+)(/[^@|]+)?([@|].+)?$")
-        m = pattern.match(path)
-        assert m, f"Cannot extract package name from github path {path}"
-        name = m.groups()[1]
-        install_cmd = f"remotes::install_github('{path}', lib='{dest}', upgrade='never')"
-    elif repo == "bitbucket":
-        path = name
-        pattern = re.compile("^([^/]+)/([^/]+)([/@].+)?$")
-        m = pattern.match(path)
-        assert m, f"Cannot extract package name from bitbucket path {path}"
-        name = m.groups()[1]
-        install_cmd = f"remotes::install_bitbucket('{path}', lib='{dest}', upgrade='never')"
-    elif repo == "local":
-        path = name
-        pattern = re.compile("^(.+?)(\\.(zip|tar(\\.(gz|bz2))?|tgz2?|tbz))?$")
-        m = pattern.match(os.path.basename(path))
-        assert m, f"Cannot extract package name from local filesystem path {path}"
-        name = m.groups()[0]
-        install_cmd = f"remotes::install_local('{path}', lib='{dest}', upgrade='never')"
-    else:
-        install_cmd = None
-
+    match repository:
+        case "cran":
+            install_cmd = f"install.packages('{name}', lib='{dest}', repos='https://cloud.r-project.org', update=FALSE, ask=FALSE)"
+        case "bioconductor":
+            install_cmd = f"BiocManager::install('{name}', lib='{dest}', update=FALSE, ask=FALSE)"
+        case "github":
+            assert url, f"Can't install R package '{name}' from github, URL is missing"
+            install_cmd = f"remotes::install_github('{url}', lib='{dest}', upgrade='never')"
+        case "bitbucket":
+            assert url, f"Can't install R package '{name}' from bitbucket, URL is missing"
+            install_cmd = f"remotes::install_bitbucket('{url}', lib='{dest}', upgrade='never')"
+        case "local":
+            assert url, f"Can't install local R package '{name}', missing path"
+            assert os.path.exists(url), f"Can't find local R package '{name}' at location '{url}'"
+            install_cmd = (
+                f"install.packages('{url}', repos=NULL, lib='{dest}', update=FALSE, ask=FALSE)"
+            )
+        case _:
+            raise ValueError("Unknown repository '{repository}'")
     R_script = [
+        f".libPaths(c(.libPaths(), '{dest}'))",
         install_cmd,
         f"status <- try(find.package('{name}', lib.loc='{dest}', quiet=FALSE, verbose=TRUE))",
         "status <- ifelse(is(status, 'try-error'), 1, 0)",
         "quit(save='no', status=status, runLast=FALSE)",
     ]
     cmd = ["R", "--vanilla", "-e", "; ".join(R_script)]
     return subprocess.run(cmd, text=True, check=True)
+
+
+def install_R_packages(dest: str, filename: str):
+    with open(filename, "rt") as f:
+        packages = json.load(f)
+    for package in packages:
+        status = install_R_package(
+            dest,
+            name=package["name"],
+            repository=package["repository"],
+            url=package.get("url", None),
+        )
+        status.check_returncode()

snappy_wrappers/wrappers/conftest.py

@@ -0,0 +1 @@
+../../tests/snappy_pipeline/workflows/conftest.py

snappy_wrappers/wrappers/sequenza/install/R_environment.json

@@ -0,0 +1,16 @@
+[
+    {
+        "name": "RcppArmadillo",
+        "repository": "cran"
+    },
+    {
+        "name": "Runuran",
+        "repository": "cran"
+    },
+    {
+        "name": "sequenza",
+        "repository": "bitbucket",
+        "url": "sequenzatools/sequenza@07116cc"
+    }
+]
+

snappy_wrappers/wrappers/sequenza/install/environment.yaml

@@ -3,17 +3,15 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - python==3.9.19
-  - r-base==4.3.3
+  - r-base==4.4.2
   - r-remotes==2.5.0
   # sequenza requirements (+copynumber)
-  - r-pbapply==1.7_2
-  - r-squash==1.0.9
-  - r-iotools==0.3_2  # See https://groups.google.com/g/sequenza-user-group/c/UA5bBNBeN18?pli=1
-  - r-readr==2.1.5
+  - r-tidyverse==2.0.0
+  - r-rcpp==1.0.14
+  - r-rcppprogress==0.4.2
+  - r-iotools==0.3.5
+  - r-pbapply==1.7.2
   - r-seqminer==9.4
-  - r-data.table==1.15.2
-  # copynumber requirements
-  - bioconductor-s4vectors==0.40.2
-  - bioconductor-iranges==2.36.0
-  - bioconductor-genomicranges==1.54.1
+  - r-ks==1.14.3
+  - r-squash==1.0.9
+

snappy_wrappers/wrappers/sequenza/install/wrapper.py

@@ -2,21 +2,25 @@
 """Installation of sequenza non-standard packages"""
 
 import os
-from pathlib import Path
 import sys
 
+from pathlib import Path
+
 # The following is required for being able to import snappy_wrappers modules
 # inside wrappers.  These run in an "inner" snakemake process which uses its
 # own conda environment which cannot see the snappy_pipeline installation.
-base_dir = os.path.normpath(os.path.join(os.path.dirname(__file__), "..", "..", "..", ".."))
-sys.path.insert(0, base_dir)
 
-from snappy_wrappers.utils import install_R_package  # noqa: E402
+
+
+base_dir = os.path.abspath(os.path.dirname(__file__))
+while os.path.basename(base_dir) != "snappy_wrappers":
+    base_dir = os.path.dirname(base_dir)
+sys.path.insert(0, os.path.dirname(base_dir))
+
+from snappy_wrappers.utils import install_R_packages
 
 __author__ = "Eric Blanc <eric.blanc@bih-charite.de>"
 
 dest = os.path.dirname(str(snakemake.output.done))
-for package in snakemake.params.packages:
-    install_R_package(dest, package["name"], package["repo"])
-
-Path(str(snakemake.output.done)).touch()
+install_R_packages(dest, os.path.join(os.path.dirname(__file__), "R_environment.json"))
+Path(snakemake.output.done).touch()

snappy_wrappers/wrappers/sequenza/run/wrapper.py

@@ -76,11 +76,11 @@ def config_to_r(x):
 
 # Follow sequenza documentation https://bitbucket.org/sequenzatools/sequenza/src/master/
 args <- list(file="{snakemake.input.seqz}", assembly="{config[assembly]}", chromosome.list={contigs})
-args <- c(args, {args_extract})
+#args <- c(args, {args_extract})
 seqz <- do.call(sequenza.extract, args=args)
 
 args <- list(sequenza.extract=seqz, chromosome.list={contigs}, mc.cores=1)
-args <- c(args, {args_fit})
+#args <- c(args, {args_fit})
 CP <- do.call(sequenza.fit, args=args)
 
 sequenza.results(sequenza.extract=seqz, cp.table=CP, sample.id="{snakemake.wildcards[library_name]}", out.dir=dirname("{snakemake.output.done}"))

tests/snappy_wrappers/wrappers/test_install_R_package.py

@@ -1,17 +1,44 @@
 # -*- coding: utf-8 -*-
 """Code for testing the R package installation helper function"""
 
-from snappy_wrappers.utils import install_R_package
+from snappy_wrappers.utils import install_R_package, install_R_packages
 
+R_packages_json = r"""[
+    {
+        "name": "cran",
+        "repository": "cran"
+    },
+    {
+        "name": "bioc",
+        "repository": "bioconductor"
+    },
+    {
+        "name": "package",
+        "repository": "github",
+        "url": "username/package/subdir@*rel.ea.se"
+    },
+    {
+        "name": "package",
+        "repository": "bitbucket",
+        "url": "username/package@ref"
+    },
+    {
+        "name": "package",
+        "repository": "local",
+        "url": "/path/to/package.tar.gz"
+    }
+]"""
 
-def test_install_R_package(mocker, fp):
+def test_install_R_packages(mocker, fp, fs):
     """Tests install_R_package"""
     mocker.patch("snappy_wrappers.utils.os.makedirs", return_value=True)
+    fs.create_file("/path/to/package.tar.gz")
+    fs.create_file("/path/to/json", contents=R_packages_json)
     packages = [
         {
             "name": "cran",
             "repo": "cran",
-            "install": "install.packages('{}', lib='/path/to/lib', update=FALSE, ask=FALSE)",
+            "install": "install.packages('{}', lib='/path/to/lib', repos='https://cloud.r-project.org', update=FALSE, ask=FALSE)",
             "check": "find.package('cran', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)",
         },
         {
@@ -21,32 +48,36 @@ def test_install_R_package(mocker, fp):
             "check": "find.package('bioc', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)",
         },
         {
-            "name": "username/package/subdir@*rel.ea.se",
+            "name": "package",
+            "url": "username/package/subdir@*rel.ea.se",
             "repo": "github",
             "install": "remotes::install_github('{}', lib='/path/to/lib', upgrade='never')",
             "check": "find.package('package', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)",
         },
         {
-            "name": "username/package/subdir@ref",
+            "name": "package",
+            "url": "username/package@ref",
             "repo": "bitbucket",
             "install": "remotes::install_bitbucket('{}', lib='/path/to/lib', upgrade='never')",
             "check": "find.package('package', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)",
         },
         {
-            "name": "/path/to/package.tar.gz",
+            "name": "package",
+            "url": "/path/to/package.tar.gz",
             "repo": "local",
-            "install": "remotes::install_local('{}', lib='/path/to/lib', upgrade='never')",
+            "install": "install.packages('{}', repos=NULL, lib='/path/to/lib', update=FALSE, ask=FALSE)",
             "check": "find.package('package', lib.loc='/path/to/lib', quiet=FALSE, verbose=TRUE)",
         },
     ]
     for package in packages:
         script = "; ".join(
             [
-                package["install"].format(package["name"]),
+                ".libPaths(c(.libPaths(), '/path/to/lib'))",
+                package["install"].format(package.get("url", package["name"])),
                 "status <- try({})".format(package["check"]),
                 "status <- ifelse(is(status, 'try-error'), 1, 0)",
                 "quit(save='no', status=status, runLast=FALSE)",
             ]
         )
         fp.register_subprocess(["R", "--vanilla", "-e", script], stdout="")
-        install_R_package(dest="/path/to/lib", name=package["name"], repo=package["repo"])
+    install_R_packages(dest="/path/to/lib", filename="/path/to/json")