Mercurial > repos > rhpvorderman > shm_csr

changeset 3:dced6d52d218 draft

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"planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
author rhpvorderman
date Mon, 15 Nov 2021 11:35:18 +0000
parents 72d68e2e1fd3
children c8f02bce10d0
files CHANGELOG.md remove_files.txt shm_csr.xml tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc tests/test_shm_csr.py wrapper.sh
diffstat 6 files changed, 206 insertions(+), 186 deletions(-) [+]
line wrap: on
line diff
--- a/CHANGELOG.md	Fri Nov 05 14:43:13 2021 +0000
+++ b/CHANGELOG.md	Mon Nov 15 11:35:18 2021 +0000
@@ -1,3 +1,15 @@
+version 1.3.2
+-------------
++ Fix a bug where the file removal process caused errors.
+
+version 1.3.1
+-------------
++ Fix issues with container discovery
+
+version 1.3.0
+-------------
++ Add missing dependencies to the requirements section.
+
 version 1.2.0
 -------------
 + Add a container in which the tool can execute.
--- a/remove_files.txt	Fri Nov 05 14:43:13 2021 +0000
+++ b/remove_files.txt	Mon Nov 15 11:35:18 2021 +0000
@@ -1,171 +1,160 @@
-results/aa_histogram.txt
-results/aa_histogram_absent.txt
-results/aa_histogram_absent_IGA.txt
-results/aa_histogram_absent_IGG.txt
-results/aa_histogram_absent_IGM.txt
-results/aa_histogram_count.txt
-results/aa_histogram_count_IGA.txt
-results/aa_histogram_count_IGG.txt
-results/aa_histogram_count_IGM.txt
-results/aa_histogram_IGA.txt
-results/aa_histogram_IGG.txt
-results/aa_histogram_IGM.txt
-results/after_unique_filter.txt
-results/all_mean_n.txt
-results/all_mean_value.txt
-results/all_median_n.txt
-results/all_median_value.txt
-results/all_sum_n.txt
-results/all_sum_value.txt
-results/before_filters.txt
-results/before_unique_filter.txt
-results/data_sum.txt
-results/filtering_steps.txt
-results/hotspot_analysis_mean.txt
-results/hotspot_analysis_median.txt
-results/hotspot_analysis_sum.txt
-results/identified_genes.txt
-results/IGA1_mean_n.txt
-results/IGA1_mean_value.txt
-results/IGA1_median_n.txt
-results/IGA1_median_value.txt
-results/IGA1_sum_n.txt
-results/IGA1_sum_value.txt
-results/IGA2_mean_n.txt
-results/IGA2_mean_value.txt
-results/IGA2_median_n.txt
-results/IGA2_median_value.txt
-results/IGA2_sum_n.txt
-results/IGA2_sum_value.txt
-results/IGA_mean_n.txt
-results/IGA_mean_value.txt
-results/IGA_median_n.txt
-results/IGA_median_value.txt
-results/IGA_sum_n.txt
-results/IGA_sum_value.txt
-results/IGE_mean_n.txt
-results/IGE_mean_value.txt
-results/IGE_median_n.txt
-results/IGE_median_value.txt
-results/IGE_sum_n.txt
-results/IGE_sum_value.txt
-results/IGG1_mean_n.txt
-results/IGG1_mean_value.txt
-results/IGG1_median_n.txt
-results/IGG1_median_value.txt
-results/IGG1_sum_n.txt
-results/IGG1_sum_value.txt
-results/IGG2_mean_n.txt
-results/IGG2_mean_value.txt
-results/IGG2_median_n.txt
-results/IGG2_median_value.txt
-results/IGG2_sum_n.txt
-results/IGG2_sum_value.txt
-results/IGG3_mean_n.txt
-results/IGG3_mean_value.txt
-results/IGG3_median_n.txt
-results/IGG3_median_value.txt
-results/IGG3_sum_n.txt
-results/IGG3_sum_value.txt
-results/IGG4_mean_n.txt
-results/IGG4_mean_value.txt
-results/IGG4_median_n.txt
-results/IGG4_median_value.txt
-results/IGG4_sum_n.txt
-results/IGG4_sum_value.txt
-results/IGG_mean_n.txt
-results/IGG_mean_value.txt
-results/IGG_median_n.txt
-results/IGG_median_value.txt
-results/IGG_sum_n.txt
-results/IGG_sum_value.txt
-results/IGM_mean_n.txt
-results/IGM_mean_value.txt
-results/IGM_median_n.txt
-results/IGM_median_value.txt
-results/IGM_sum_n.txt
-results/IGM_sum_value.txt
-results/matched_all_mean.txt
-results/matched_all_median.txt
-results/matched_IGA1_mean.txt
-results/matched_IGA1_median.txt
-results/matched_IGA2_mean.txt
-results/matched_IGA2_median.txt
-results/matched_IGA_mean.txt
-results/matched_IGA_median.txt
-results/matched_IGE_mean.txt
-results/matched_IGE_median.txt
-results/matched_IGG1_mean.txt
-results/matched_IGG1_median.txt
-results/matched_IGG2_mean.txt
-results/matched_IGG2_median.txt
-results/matched_IGG3_mean.txt
-results/matched_IGG3_median.txt
-results/matched_IGG4_mean.txt
-results/matched_IGG4_median.txt
-results/matched_IGG_mean.txt
-results/matched_IGG_median.txt
-results/matched_IGM_mean.txt
-results/matched_IGM_median.txt
-results/matched_unmatched_mean.txt
-results/matched_unmatched_median.txt
-results/matched_unmatched_sum.txt
-results/mutationdict.txt
-results/mutation_in_motifs.txt
-results/mutations_mean.txt
-results/mutations_median.txt
-results/mutations_sum.txt
-results/RGYW.txt
-results/shm_overview_tandem_row.txt
-results/tandem_frequency.txt
-results/transitions_all_mean.txt
-results/transitions_all_median.txt
-results/transitions_IGA1_mean.txt
-results/transitions_IGA1_median.txt
-results/transitions_IGA2_mean.txt
-results/transitions_IGA2_median.txt
-results/transitions_IGA_mean.txt
-results/transitions_IGA_median.txt
-results/transitions_IGE_mean.txt
-results/transitions_IGE_median.txt
-results/transitions_IGG1_mean.txt
-results/transitions_IGG1_median.txt
-results/transitions_IGG2_mean.txt
-results/transitions_IGG2_median.txt
-results/transitions_IGG3_mean.txt
-results/transitions_IGG3_median.txt
-results/transitions_IGG4_mean.txt
-results/transitions_IGG4_median.txt
-results/transitions_IGG_mean.txt
-results/transitions_IGG_median.txt
-results/transitions_IGM_mean.txt
-results/transitions_IGM_median.txt
-results/transitions_unmatched_mean.txt
-results/transitions_unmatched_median.txt
-results/transitions_unmatched_sum.txt
-results/unmatched_mean_n.txt
-results/unmatched_mean_value.txt
-results/unmatched_median_n.txt
-results/unmatched_median_value.txt
-results/unmatched_sum_n.txt
-results/unmatched_sum_value.txt
-results/change_o/change-o-db.txt
-results/change_o/change-o-db-defined_first_clones.txt
-results/change_o/change-o-db-defined_first_clones-IGA.txt
-results/change_o/change-o-db-defined_first_clones-IGG.txt
-results/change_o/change-o-db-defined_first_clones-IGM.txt
-results/change_o/change-o-db-IGA.txt
-results/change_o/change-o-db-IGG.txt
-results/change_o/change-o-db-IGM.txt
-results/change_o/input.tab
-aa.txt
-aa_change_stats.txt
-gapped_aa.txt
-gapped_nt.txt
-hotspots.txt
-junction.txt
-mutationanalysis.txt
-mutationstats.txt
-sequences.txt
-summary.txt
-Rplots.pdf
+aa_histogram.txt
+aa_histogram_absent.txt
+aa_histogram_absent_IGA.txt
+aa_histogram_absent_IGG.txt
+aa_histogram_absent_IGM.txt
+aa_histogram_count.txt
+aa_histogram_count_IGA.txt
+aa_histogram_count_IGG.txt
+aa_histogram_count_IGM.txt
+aa_histogram_IGA.txt
+aa_histogram_IGG.txt
+aa_histogram_IGM.txt
+after_unique_filter.txt
+all_mean_n.txt
+all_mean_value.txt
+all_median_n.txt
+all_median_value.txt
+all_sum_n.txt
+all_sum_value.txt
+before_filters.txt
+before_unique_filter.txt
+data_sum.txt
+filtering_steps.txt
+hotspot_analysis_mean.txt
+hotspot_analysis_median.txt
+hotspot_analysis_sum.txt
+identified_genes.txt
+IGA1_mean_n.txt
+IGA1_mean_value.txt
+IGA1_median_n.txt
+IGA1_median_value.txt
+IGA1_sum_n.txt
+IGA1_sum_value.txt
+IGA2_mean_n.txt
+IGA2_mean_value.txt
+IGA2_median_n.txt
+IGA2_median_value.txt
+IGA2_sum_n.txt
+IGA2_sum_value.txt
+IGA_mean_n.txt
+IGA_mean_value.txt
+IGA_median_n.txt
+IGA_median_value.txt
+IGA_sum_n.txt
+IGA_sum_value.txt
+IGE_mean_n.txt
+IGE_mean_value.txt
+IGE_median_n.txt
+IGE_median_value.txt
+IGE_sum_n.txt
+IGE_sum_value.txt
+IGG1_mean_n.txt
+IGG1_mean_value.txt
+IGG1_median_n.txt
+IGG1_median_value.txt
+IGG1_sum_n.txt
+IGG1_sum_value.txt
+IGG2_mean_n.txt
+IGG2_mean_value.txt
+IGG2_median_n.txt
+IGG2_median_value.txt
+IGG2_sum_n.txt
+IGG2_sum_value.txt
+IGG3_mean_n.txt
+IGG3_mean_value.txt
+IGG3_median_n.txt
+IGG3_median_value.txt
+IGG3_sum_n.txt
+IGG3_sum_value.txt
+IGG4_mean_n.txt
+IGG4_mean_value.txt
+IGG4_median_n.txt
+IGG4_median_value.txt
+IGG4_sum_n.txt
+IGG4_sum_value.txt
+IGG_mean_n.txt
+IGG_mean_value.txt
+IGG_median_n.txt
+IGG_median_value.txt
+IGG_sum_n.txt
+IGG_sum_value.txt
+IGM_mean_n.txt
+IGM_mean_value.txt
+IGM_median_n.txt
+IGM_median_value.txt
+IGM_sum_n.txt
+IGM_sum_value.txt
+matched_all_mean.txt
+matched_all_median.txt
+matched_IGA1_mean.txt
+matched_IGA1_median.txt
+matched_IGA2_mean.txt
+matched_IGA2_median.txt
+matched_IGA_mean.txt
+matched_IGA_median.txt
+matched_IGE_mean.txt
+matched_IGE_median.txt
+matched_IGG1_mean.txt
+matched_IGG1_median.txt
+matched_IGG2_mean.txt
+matched_IGG2_median.txt
+matched_IGG3_mean.txt
+matched_IGG3_median.txt
+matched_IGG4_mean.txt
+matched_IGG4_median.txt
+matched_IGG_mean.txt
+matched_IGG_median.txt
+matched_IGM_mean.txt
+matched_IGM_median.txt
+matched_unmatched_mean.txt
+matched_unmatched_median.txt
+matched_unmatched_sum.txt
+mutationdict.txt
+mutation_in_motifs.txt
+mutations_mean.txt
+mutations_median.txt
+mutations_sum.txt
+RGYW.txt
+shm_overview_tandem_row.txt
+tandem_frequency.txt
+transitions_all_mean.txt
+transitions_all_median.txt
+transitions_IGA1_mean.txt
+transitions_IGA1_median.txt
+transitions_IGA2_mean.txt
+transitions_IGA2_median.txt
+transitions_IGA_mean.txt
+transitions_IGA_median.txt
+transitions_IGE_mean.txt
+transitions_IGE_median.txt
+transitions_IGG1_mean.txt
+transitions_IGG1_median.txt
+transitions_IGG2_mean.txt
+transitions_IGG2_median.txt
+transitions_IGG3_mean.txt
+transitions_IGG3_median.txt
+transitions_IGG4_mean.txt
+transitions_IGG4_median.txt
+transitions_IGG_mean.txt
+transitions_IGG_median.txt
+transitions_IGM_mean.txt
+transitions_IGM_median.txt
+transitions_unmatched_mean.txt
+transitions_unmatched_median.txt
+transitions_unmatched_sum.txt
+unmatched_mean_n.txt
+unmatched_mean_value.txt
+unmatched_median_n.txt
+unmatched_median_value.txt
+unmatched_sum_n.txt
+unmatched_sum_value.txt
+change_o/change-o-db.txt
+change_o/change-o-db-defined_first_clones.txt
+change_o/change-o-db-defined_first_clones-IGA.txt
+change_o/change-o-db-defined_first_clones-IGG.txt
+change_o/change-o-db-defined_first_clones-IGM.txt
+change_o/change-o-db-IGA.txt
+change_o/change-o-db-IGG.txt
+change_o/change-o-db-IGM.txt
+change_o/input.tab
--- a/shm_csr.xml	Fri Nov 05 14:43:13 2021 +0000
+++ b/shm_csr.xml	Mon Nov 15 11:35:18 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.3.1">
+<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.3.2">
 	<description></description>
 	<requirements>
 		<requirement type="package" version="3.7.1">python</requirement>
Binary file tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc has changed
--- a/tests/test_shm_csr.py	Fri Nov 05 14:43:13 2021 +0000
+++ b/tests/test_shm_csr.py	Mon Nov 15 11:35:18 2021 +0000
@@ -36,11 +36,17 @@
 
 @pytest.fixture(scope="module")
 def shm_csr_result():
-    temp_dir = tempfile.mktemp()
-    shutil.copytree(GIT_ROOT, temp_dir)
+    temp_dir = Path(tempfile.mkdtemp())
+    tool_dir = temp_dir / "shm_csr"
+    shutil.copytree(GIT_ROOT, tool_dir)
+    working_dir = temp_dir / "working"
+    working_dir.mkdir(parents=True)
+    output_dir = temp_dir / "outputs"
+    output_dir.mkdir(parents=True)
+    wrapper = str(tool_dir / "wrapper.sh")
     input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
-    out_files_path = os.path.join(temp_dir, "results")
-    out_file = os.path.join(out_files_path, "result.html")
+    out_files_path = output_dir / "results"
+    out_file = out_files_path / "result.html"
     infile_name = "input_data"
     functionality = "productive"
     unique = "Sequence.ID"
@@ -57,11 +63,11 @@
     fast = 'no'
     cmd = [
         "bash",
-        "wrapper.sh",
+        wrapper,
         input,
         "custom",
-        out_file,
-        out_files_path,
+        str(out_file),
+        str(out_files_path),
         infile_name,
         "-",
         functionality,
@@ -78,8 +84,10 @@
         empty_region_filter,
         fast
     ]
-    subprocess.run(cmd, cwd=temp_dir, stdout=sys.stdout, stderr=sys.stderr,
-                   check=True)
+    with open(temp_dir / "stderr", "wt") as stderr_file:
+        with open(temp_dir / "stdout", "wt") as stdout_file:
+            subprocess.run(cmd, cwd=working_dir, stdout=stdout_file,
+                           stderr=stderr_file, check=True)
     yield Path(out_files_path)
     #shutil.rmtree(temp_dir)
 
--- a/wrapper.sh	Fri Nov 05 14:43:13 2021 +0000
+++ b/wrapper.sh	Mon Nov 15 11:35:18 2021 +0000
@@ -895,15 +895,26 @@
 echo "---------------- remove_files----------------"
 echo "---------------- remove_files----------------<br />" >> $log
 
-rm -r -v -f results/baseline
-rm -r -v -f files
-filename='remove_files.txt'
+rm -r -v -f $outdir/baseline
+rm -r -v -f $PWD/files
+rm -v $PWD/aa.txt
+rm -v $PWD/aa_change_stats.txt
+rm -v $PWD/gapped_aa.txt
+rm -v $PWD/gapped_nt.txt
+rm -v $PWD/hotspots.txt
+rm -v $PWD/junction.txt
+rm -v $PWD/mutationanalysis.txt
+rm -v $PWD/mutationstats.txt
+rm -v $PWD/sequences.txt
+rm -v $PWD/summary.txt
+rm -v $PWD/Rplots.pdf
+
+filename="$dir/remove_files.txt"
 
 while read file; do
-    rm -v -f $file
+    rm -v -f $outdir/$file
 done < "$filename"
 
-
 echo "---------------- Done! ----------------"
 echo "---------------- Done! ----------------<br />" >> $outdir/log.html