Merge remote-tracking branch 'origin/test' into prod

ncbi · Aug 10, 2022 · bd40b1d · bd40b1d
2 parents f8c8990 + 733ab71
commit bd40b1d
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Showing 2 changed files with 19 additions and 39 deletions.
diff --git a/progs/align_filter.cwl b/progs/align_filter.cwl
@@ -4,44 +4,14 @@ label: "align_filter"
 class: CommandLineTool
 
 baseCommand: align_filter
-# this is only one example
-# 
-# 
-# 
-# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2018-03-13.build2663/bin/align_filter \
-#     -onon-match \
-#     /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/align_filter_sa.455675142/out/align-nomatch.asn \
-#     -asn-cache \
-#     /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/sequence_cache \
-#     -filter \
-#     'pct_coverage \
-#     >= \
-#     20' \
-#     -ifmt \
-#     seq-align \
-#     -input-manifest \
-#     /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/align_filter_sa.455675142/inp/align.mft \
-#     -logfile \
-#     /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/align_filter_sa.455675142/log/align_filter.log \
-#     -o \
-#     /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/align_filter_sa.455675142/out/align.asn
-# 
-# 
-# 
-# /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/system/2018-03-13.build2663/bin/gp_register_stats \
-#     -ifmt \
-#     seq-align \
-#     -input \
-#     /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/bacterial_pipeline/data56/Mycoplasma_genitalium_G37/Mycoplasma_genitalium_External_PGAP.4585524/4829637/align_filter_sa.455675142/out/align.asn
-# 
-# 
-# 
 requirements:
   - class: InlineJavascriptRequirement
   - class: InitialWorkDirRequirement
     listing:
      - entryname: aligns.mft
        entry: ${var blob = '# aligns.mft created for align_filter from input "input" Array of Files\n'; for (var i = 0; i < inputs.input.length; i++) { blob += inputs.input[i].path + '\n'; } return blob; }
+     - entryname: subject_allowlist.mft
+       entry: ${var blob = '# subject_allowlist.mft created for align_filter from input "subject_allowlist" File\n'; if ( inputs.subject_allowlist == null) { return blob; } else { blob += inputs.subject_allowlist.path + '\n';  return blob; }}
 
 inputs:
   asn_cache:
@@ -71,6 +41,9 @@ inputs:
       prefix: -nogenbank
   subject_allowlist: 
     type: File?
+  subject_allowlist_mft:
+    type: string?
+    default: subject_allowlist.mft
     inputBinding:
       prefix: -subject-allowlist
   onon_match_name: 

diff --git a/scripts/pgap.py b/scripts/pgap.py
@@ -174,9 +174,9 @@ def __init__(self, params, local_input, pipeline):
         else:
             self.submol = None
         self.yaml = self.create_inputfile(local_input)
-        if (self.params.docker_type == 'singularity'):
+        if self.params.docker_type in ['singularity', 'apptainer']:
             self.make_singularity_cmd()
-        elif (self.params.docker_type == 'podman'):
+        elif self.params.docker_type == 'podman':
             self.make_podman_cmd()
         else:
             self.make_docker_cmd()
@@ -395,7 +395,7 @@ def check_runtime_setting(settings, value, min):
             if settings[value] != 'unlimited' and settings[value] < min:
                 print('WARNING: {} is less than the recommended value of {}'.format(value, min))
 
-        if (self.params.docker_type == 'singularity'):
+        if (self.params.docker_type in ['singularity', 'apptainer']):
             singularity_docker_image = self.params.docker_image if self.params.args.container_path else "docker://"+self.params.docker_image
             cmd = [self.params.docker_cmd, 'exec', '--bind', '{}:/cwd:ro'.format(os.getcwd()), singularity_docker_image,
                    'bash', '-c', 'df -k /cwd /tmp ; ulimit -a ; cat /proc/{meminfo,cpuinfo}']
@@ -486,7 +486,12 @@ def __init__(self, args):
         self.ani_hr_output = None
         self.branch          = self.get_branch()
         self.repo            = self.get_repo()
-        self.install_dir     = os.environ.get('PGAP_INPUT_DIR',os.environ['HOME']+'/.pgap')
+
+        if platform.system() == 'Windows':
+            self.install_dir     = os.environ.get('PGAP_INPUT_DIR',os.environ['USERPROFILE']+'/.pgap')
+        else:
+            self.install_dir     = os.environ.get('PGAP_INPUT_DIR',os.environ['HOME']+'/.pgap')
+
         self.local_version   = self.get_local_version()
         if self.args.no_internet:
             self.remote_versions = [self.local_version]
@@ -604,7 +609,7 @@ def get_output_dir(self):
         return outputdir
 
     def get_docker_info(self):
-        docker_type_alternatives = ['docker', 'podman', 'singularity']
+        docker_type_alternatives = ['docker', 'podman', 'singularity', 'apptainer']
         if self.args.docker:
             self.docker_cmd = shutil.which(self.args.docker)
         else:
@@ -653,6 +658,8 @@ def str2sec(s):
         return str2sec(self.args.timeout)
 
     def update(self):
+        print(f"installation directory: {self.install_dir}")
+        subprocess.run(["/bin/df", "-k", self.install_dir])
         self.update_self()
         threads = list()
         docker_thread = mp.Process(target = self.install_docker, name='docker image pull')
@@ -674,7 +681,7 @@ def update(self):
         self.write_version()
 
     def install_docker(self):
-        if self.docker_type == 'singularity':
+        if self.docker_type in ['singularity', 'apptainer']:
             sif = self.docker_image.replace("ncbi/pgap:", "pgap_") + ".sif"
             try:
                 subprocess.run([self.docker_cmd, 'sif', 'list', sif],
@@ -847,7 +854,7 @@ def main():
                         If flag is set, run  ANI first, then PGAP, overriding the organism name provided by the user in the input YAML with the value returned by ANI Predicted organism. Obviously both actions need to be requested for this flag to take effect
                         ''')
     parser.add_argument('-D', '--docker', metavar='path',
-                        help='Docker-compatible executable (e.g. docker, podman, singularity), which may include a full path like /usr/bin/docker')
+                        help='Docker-compatible executable (e.g. docker, podman, apptainer), which may include a full path like /usr/bin/docker')
     parser.add_argument('-o', '--output', metavar='path', default='output',
                         help='Output directory to be created, which may include a full path')
     parser.add_argument('-t', '--timeout', default='24:00:00', help=argparse.SUPPRESS)