changeset 84:4db34e32dd47 draft

"planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
author rhpvorderman
date Wed, 27 Oct 2021 09:38:20 +0000
parents 729738462297
children a539d14d66b6
files CHANGELOG.md conda_environment.yml container/involucro remove_files.txt shm_csr.xml tests/.pytest_cache/.gitignore tests/.pytest_cache/CACHEDIR.TAG tests/.pytest_cache/README.md tests/.pytest_cache/v/cache/nodeids tests/.pytest_cache/v/cache/stepwise tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.4.pyc tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc wrapper.sh
diffstat 13 files changed, 191 insertions(+), 36 deletions(-) [+]
line wrap: on
line diff
--- a/CHANGELOG.md	Wed Sep 15 12:24:06 2021 +0000
+++ b/CHANGELOG.md	Wed Oct 27 09:38:20 2021 +0000
@@ -1,3 +1,8 @@
+version 1.2.0
+-------------
++ Add a container in which the tool can execute.
++ Remove redundant files after execution.
+
 version 1.1.0
 -------------
 + Added changeo as a dependency. Porting to python3 was necessary to achieve 
--- a/conda_environment.yml	Wed Sep 15 12:24:06 2021 +0000
+++ b/conda_environment.yml	Wed Oct 27 09:38:20 2021 +0000
@@ -4,7 +4,7 @@
   - bioconda
   - defaults
 dependencies:
-  - python=3.7
+  - python=3.7.1
   - changeo=0.4.4
   - biopython=1.72  # Higher versions break changeo
   - unzip=6.0
Binary file container/involucro has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/remove_files.txt	Wed Oct 27 09:38:20 2021 +0000
@@ -0,0 +1,171 @@
+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
--- a/shm_csr.xml	Wed Sep 15 12:24:06 2021 +0000
+++ b/shm_csr.xml	Wed Oct 27 09:38:20 2021 +0000
@@ -1,7 +1,7 @@
-<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.1">
+<tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.2">
 	<description></description>
 	<requirements>
-		<requirement type="package" version="3.7">python</requirement>
+		<requirement type="package" version="3.7.1">python</requirement>
 		<requirement type="package" version="0.4.4">changeo</requirement>
 		<!--Biopython should be set at a version at the release of changeo 0.4.4.
 		 Later versions of biopython break changeo 0.4.4 because of the Alphabet deprecation.-->
@@ -16,6 +16,7 @@
 		<requirement type="package" version="4.4.18">bash</requirement>
 		<requirement type="package" version="1.34">tar</requirement>
 		<requirement type="package" version="5.39">file</requirement>
+		<container type="docker">quay.io/rhpvorderman/mulled-v2-a2524529ff4c0254c944ff4606e926ca2e8b80d0:9fa3e7fda79c80bf1af596872bddd871913a2c1c-0</container>
 	</requirements>
 	<command interpreter="bash">
 		#if str ( $filter_unique.filter_unique_select ) == "remove":
--- a/tests/.pytest_cache/.gitignore	Wed Sep 15 12:24:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-# Created by pytest automatically.
-*
--- a/tests/.pytest_cache/CACHEDIR.TAG	Wed Sep 15 12:24:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Signature: 8a477f597d28d172789f06886806bc55
-# This file is a cache directory tag created by pytest.
-# For information about cache directory tags, see:
-#	http://www.bford.info/cachedir/spec.html
--- a/tests/.pytest_cache/README.md	Wed Sep 15 12:24:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-# pytest cache directory #
-
-This directory contains data from the pytest's cache plugin,
-which provides the `--lf` and `--ff` options, as well as the `cache` fixture.
-
-**Do not** commit this to version control.
-
-See [the docs](https://docs.pytest.org/en/stable/cache.html) for more information.
--- a/tests/.pytest_cache/v/cache/nodeids	Wed Sep 15 12:24:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-[
-  "test_shm_csr.py::test_aa_histogram_sum"
-]
\ No newline at end of file
--- a/tests/.pytest_cache/v/cache/stepwise	Wed Sep 15 12:24:06 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-[]
\ No newline at end of file
Binary file tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.4.pyc has changed
Binary file tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc has changed
--- a/wrapper.sh	Wed Sep 15 12:24:06 2021 +0000
+++ b/wrapper.sh	Wed Oct 27 09:38:20 2021 +0000
@@ -892,6 +892,17 @@
 
 IFS="$tIFS"
 
+echo "---------------- remove_files----------------"
+echo "---------------- remove_files----------------<br />" >> $log
+
+rm -r -v results/baseline
+rm -r -v files
+filename='remove_files.txt'
+
+while read file; do
+    rm -v $file
+done < "$filename"
+
 
 echo "---------------- Done! ----------------"
 echo "---------------- Done! ----------------<br />" >> $outdir/log.html
@@ -901,18 +912,3 @@
 
 
 
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