gtdbtk, fix py env + chmod pigz

hallamlab · May 2, 2023 · d24ef55 · d24ef55
1 parent 55d0ad5
commit d24ef55
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Showing 7 changed files with 9 additions and 9 deletions.
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,5 @@
 
 __pycache__
 cache
+
+/lib/limes_x
diff --git a/logistics/extract_mg-reads/setup/setup.smk b/logistics/extract_mg-reads/setup/setup.smk
@@ -34,6 +34,6 @@ rule compile_pigz:
         """
         tar -xf {input} && mv pigz pigz_lib \
         && cd pigz_lib && make \
-        && cp pigz ../ && cd ../ && rm -rf pigz_lib \
+        && chmod +x pigz && cp pigz ../ && cd ../ && rm -rf pigz_lib \
         && rm {input}
         """
diff --git a/metagenomics/metagenomic_assembly/setup/setup.smk b/metagenomics/metagenomic_assembly/setup/setup.smk
@@ -39,6 +39,6 @@ rule compile_pigz:
         """
         tar -xf {input} && mv pigz pigz_lib \
         && cd pigz_lib && make \
-        && cp pigz ../ && cd ../ && rm -rf pigz_lib \
+        && chmod +x pigz && cp pigz ../ && cd ../ && rm -rf pigz_lib \
         && rm {input}
         """
diff --git a/metagenomics/metagenomic_binning/lib/definition.py b/metagenomics/metagenomic_binning/lib/definition.py
@@ -47,10 +47,6 @@ def fail(msg: str):
         assert isinstance(r, Path), f"expected path for reads, got {type(r)} for {r}"
         zipped_reads.append(r)
 
-    # rtype = context.manifest[READ_TYPE]
-    # assert isinstance(rtype, str), f"invalid read type: {rtype}"
-    # _, read_type = rtype.split(':')
-
     name = context.manifest[SAMPLE]
     assert isinstance(name, str), f"name wasn't a str: {name}"
 
@@ -77,11 +73,12 @@ def fail(msg: str):
         else:
             single = True
 
-    # https://github.com/bxlab/metaWRAP/issues/254    
+    # does not handle interleaved
     special_read_type = " "
     if single:
         special_read_type = "--single-end"
     if paired and single:
+        # https://github.com/bxlab/metaWRAP/issues/254    
         reads = [r for r in reads if not str(r).split(".")[-2].endswith("_2")]
 
     #################################################################################

diff --git a/metagenomics/metagenomic_binning/setup/setup.smk b/metagenomics/metagenomic_binning/setup/setup.smk
@@ -34,7 +34,7 @@ rule compile_pigz:
         """
         tar -xf {input} && mv pigz pigz_lib \
         && cd pigz_lib && make \
-        && cp pigz ../ && cd ../ && rm -rf pigz_lib \
+        && chmod +x pigz && cp pigz ../ && cd ../ && rm -rf pigz_lib \
         && rm {input}
         """
 

diff --git a/metagenomics/taxonomy_on_bin/lib/gtdbtk.py b/metagenomics/taxonomy_on_bin/lib/gtdbtk.py
@@ -63,6 +63,7 @@ def gtdbtk_procedure(context: JobContext, SAMPLE, BINS, GTDBTK_WS, GTDBTK_TAX, C
 
     code = context.shell(f"""\
         mkdir -p {temp_dir}
+        PYTHONPATH=""
         singularity run -B {",".join(binds)} {container} \
         gtdbtk classify_wf -x {ext} \
             --cpus {params.threads} --pplacer_cpus {int(min(params.threads, params.mem_gb//(40+1)))} \

diff --git a/metagenomics/taxonomy_on_bin/setup/setup.smk b/metagenomics/taxonomy_on_bin/setup/setup.smk
@@ -12,7 +12,7 @@ rule get_image:
         CONTAINER
     shell:
         """
-        singularity build {output} docker://quay.io/txyliu/gtdbtk
+        singularity build {output} docker://ecogenomic/gtdbtk:2.2.6
         """
 
 # check url if change version