Merge pull request #92 from fls-bioinformatics-core/trimmomatic-move-…

…to-legacy Relocate Trimmomatic tool to 'legacy' subdir
fls-bioinformatics-core · Jan 18, 2024 · 652e807 · 652e807
2 parents 9e2adcd + c87098b
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diff --git a/.github/workflows/planemo-ci-tests.yml b/.github/workflows/planemo-ci-tests.yml
@@ -14,7 +14,6 @@ jobs:
       matrix:
         # Define the tools and Galaxy versions to test
         galaxy-tool:
-          - trimmomatic
           - pal_finder
           - weeder2
           - rnachipintegrator

diff --git a/README.rst b/README.rst
@@ -19,7 +19,6 @@ The ``tools`` subdirectory contains the following tools which wrap
  * `MACS2 <https://toolshed.g2.bx.psu.edu/view/pjbriggs/macs21/>`_
  * `pal_finder <https://toolshed.g2.bx.psu.edu/view/pjbriggs/pal_finder/>`_
  * SOLiD_preprocess_filter_v2.pl
- * `trimmomatic <https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic/>`_
  * weeder
  * `weeder2 <https://toolshed.g2.bx.psu.edu/view/pjbriggs/weeder2/>`_
  * bedgraph_to_wig converter

diff --git a/legacy/README.rst b/legacy/README.rst
@@ -12,3 +12,7 @@ developed elsewhere.
  * ``rnachipintegrator``: version which pre-dates the change of format
    for the ``.loc`` file used for the "canonical genes" tool.
    Current version of the tool is in the ``tools`` subdirectory.
+
+ * ``trimmomatic``: now pushed to the
+   `galaxproject/tools-iuc (https://github.com/galaxyproject/tools-iuc)`_
+   repository (see `pull request 5698 (https://github.com/galaxyproject/tools-iuc/pull/5698)`_
diff --git a/tools/trimmomatic/.shed.yml → legacy/trimmomatic/.shed.yml b/tools/trimmomatic/.shed.yml → legacy/trimmomatic/.shed.yml
diff --git a/tools/trimmomatic/README.rst → legacy/trimmomatic/README.rst b/tools/trimmomatic/README.rst → legacy/trimmomatic/README.rst
@@ -1,6 +1,11 @@
 Trimmomatic: flexible read trimming tool for Illumina NGS data
 ==============================================================
 
+* **This data manager has been pushed to the
+  [galaxproject/tools-iuc](https://github.com/galaxyproject/tools-iuc)
+  repository (see
+  [pull request 5698](https://github.com/galaxyproject/tools-iuc/pull/5698)**
+
 Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
 manipluating Illumina FASTQ files (both single and paired-end).
 

diff --git a/tools/trimmomatic/install_tool_deps.sh → legacy/trimmomatic/install_tool_deps.sh b/tools/trimmomatic/install_tool_deps.sh → legacy/trimmomatic/install_tool_deps.sh
diff --git a/tools/trimmomatic/package_trimmomatic.sh → legacy/trimmomatic/package_trimmomatic.sh b/tools/trimmomatic/package_trimmomatic.sh → legacy/trimmomatic/package_trimmomatic.sh
diff --git a/tools/trimmomatic/run_planemo_tests.sh → legacy/trimmomatic/run_planemo_tests.sh b/tools/trimmomatic/run_planemo_tests.sh → legacy/trimmomatic/run_planemo_tests.sh
diff --git a/...rimmomatic/test-data/Illumina_SG_R1.fastq → ...rimmomatic/test-data/Illumina_SG_R1.fastq b/...rimmomatic/test-data/Illumina_SG_R1.fastq → ...rimmomatic/test-data/Illumina_SG_R1.fastq
diff --git a/...momatic/test-data/Illumina_SG_R1.fastq.gz → ...momatic/test-data/Illumina_SG_R1.fastq.gz b/...momatic/test-data/Illumina_SG_R1.fastq.gz → ...momatic/test-data/Illumina_SG_R1.fastq.gz
diff --git a/...ic/test-data/Illumina_SG_R1.fastqillumina → ...ic/test-data/Illumina_SG_R1.fastqillumina b/...ic/test-data/Illumina_SG_R1.fastqillumina → ...ic/test-data/Illumina_SG_R1.fastqillumina
diff --git a/...atic/test-data/Illumina_SG_R1.fastqsolexa → ...atic/test-data/Illumina_SG_R1.fastqsolexa b/...atic/test-data/Illumina_SG_R1.fastqsolexa → ...atic/test-data/Illumina_SG_R1.fastqsolexa
diff --git a/...rimmomatic/test-data/Illumina_SG_R2.fastq → ...rimmomatic/test-data/Illumina_SG_R2.fastq b/...rimmomatic/test-data/Illumina_SG_R2.fastq → ...rimmomatic/test-data/Illumina_SG_R2.fastq
diff --git a/...momatic/test-data/Illumina_SG_R2.fastq.gz → ...momatic/test-data/Illumina_SG_R2.fastq.gz b/...momatic/test-data/Illumina_SG_R2.fastq.gz → ...momatic/test-data/Illumina_SG_R2.fastq.gz
diff --git a/...ic/test-data/Illumina_SG_R2.fastqillumina → ...ic/test-data/Illumina_SG_R2.fastqillumina b/...ic/test-data/Illumina_SG_R2.fastqillumina → ...ic/test-data/Illumina_SG_R2.fastqillumina
diff --git a/...atic/test-data/Illumina_SG_R2.fastqsolexa → ...atic/test-data/Illumina_SG_R2.fastqsolexa b/...atic/test-data/Illumina_SG_R2.fastqsolexa → ...atic/test-data/Illumina_SG_R2.fastqsolexa
diff --git a/...matic/test-data/trimmomatic_avgqual.fastq → ...matic/test-data/trimmomatic_avgqual.fastq b/...matic/test-data/trimmomatic_avgqual.fastq → ...matic/test-data/trimmomatic_avgqual.fastq
diff --git a/...matic/test-data/trimmomatic_maxinfo.fastq → ...matic/test-data/trimmomatic_maxinfo.fastq b/...matic/test-data/trimmomatic_maxinfo.fastq → ...matic/test-data/trimmomatic_maxinfo.fastq
diff --git a/...-data/trimmomatic_pe_r1_paired_out1.fastq → ...-data/trimmomatic_pe_r1_paired_out1.fastq b/...-data/trimmomatic_pe_r1_paired_out1.fastq → ...-data/trimmomatic_pe_r1_paired_out1.fastq
diff --git a/...ta/trimmomatic_pe_r1_paired_out1.fastq.gz → ...ta/trimmomatic_pe_r1_paired_out1.fastq.gz b/...ta/trimmomatic_pe_r1_paired_out1.fastq.gz → ...ta/trimmomatic_pe_r1_paired_out1.fastq.gz
diff --git a/...immomatic_pe_r1_paired_out1.fastqillumina → ...immomatic_pe_r1_paired_out1.fastqillumina b/...immomatic_pe_r1_paired_out1.fastqillumina → ...immomatic_pe_r1_paired_out1.fastqillumina
diff --git a/...trimmomatic_pe_r1_paired_out1.fastqsolexa → ...trimmomatic_pe_r1_paired_out1.fastqsolexa b/...trimmomatic_pe_r1_paired_out1.fastqsolexa → ...trimmomatic_pe_r1_paired_out1.fastqsolexa
diff --git a/.../trimmomatic_pe_r1_paired_out1_clip.fastq → .../trimmomatic_pe_r1_paired_out1_clip.fastq b/.../trimmomatic_pe_r1_paired_out1_clip.fastq → .../trimmomatic_pe_r1_paired_out1_clip.fastq
diff --git a/...ata/trimmomatic_pe_r1_unpaired_out1.fastq → ...ata/trimmomatic_pe_r1_unpaired_out1.fastq b/...ata/trimmomatic_pe_r1_unpaired_out1.fastq → ...ata/trimmomatic_pe_r1_unpaired_out1.fastq
diff --git a/.../trimmomatic_pe_r1_unpaired_out1.fastq.gz → .../trimmomatic_pe_r1_unpaired_out1.fastq.gz b/.../trimmomatic_pe_r1_unpaired_out1.fastq.gz → .../trimmomatic_pe_r1_unpaired_out1.fastq.gz
diff --git a/...momatic_pe_r1_unpaired_out1.fastqillumina → ...momatic_pe_r1_unpaired_out1.fastqillumina b/...momatic_pe_r1_unpaired_out1.fastqillumina → ...momatic_pe_r1_unpaired_out1.fastqillumina
diff --git a/...immomatic_pe_r1_unpaired_out1.fastqsolexa → ...immomatic_pe_r1_unpaired_out1.fastqsolexa b/...immomatic_pe_r1_unpaired_out1.fastqsolexa → ...immomatic_pe_r1_unpaired_out1.fastqsolexa
diff --git a/...-data/trimmomatic_pe_r2_paired_out1.fastq → ...-data/trimmomatic_pe_r2_paired_out1.fastq b/...-data/trimmomatic_pe_r2_paired_out1.fastq → ...-data/trimmomatic_pe_r2_paired_out1.fastq
diff --git a/...ta/trimmomatic_pe_r2_paired_out1.fastq.gz → ...ta/trimmomatic_pe_r2_paired_out1.fastq.gz b/...ta/trimmomatic_pe_r2_paired_out1.fastq.gz → ...ta/trimmomatic_pe_r2_paired_out1.fastq.gz
diff --git a/...immomatic_pe_r2_paired_out1.fastqillumina → ...immomatic_pe_r2_paired_out1.fastqillumina b/...immomatic_pe_r2_paired_out1.fastqillumina → ...immomatic_pe_r2_paired_out1.fastqillumina
diff --git a/...trimmomatic_pe_r2_paired_out1.fastqsolexa → ...trimmomatic_pe_r2_paired_out1.fastqsolexa b/...trimmomatic_pe_r2_paired_out1.fastqsolexa → ...trimmomatic_pe_r2_paired_out1.fastqsolexa
diff --git a/...ata/trimmomatic_pe_r2_unpaired_out1.fastq → ...ata/trimmomatic_pe_r2_unpaired_out1.fastq b/...ata/trimmomatic_pe_r2_unpaired_out1.fastq → ...ata/trimmomatic_pe_r2_unpaired_out1.fastq
diff --git a/.../trimmomatic_pe_r2_unpaired_out1.fastq.gz → .../trimmomatic_pe_r2_unpaired_out1.fastq.gz b/.../trimmomatic_pe_r2_unpaired_out1.fastq.gz → .../trimmomatic_pe_r2_unpaired_out1.fastq.gz
diff --git a/...momatic_pe_r2_unpaired_out1.fastqillumina → ...momatic_pe_r2_unpaired_out1.fastqillumina b/...momatic_pe_r2_unpaired_out1.fastqillumina → ...momatic_pe_r2_unpaired_out1.fastqillumina
diff --git a/...immomatic_pe_r2_unpaired_out1.fastqsolexa → ...immomatic_pe_r2_unpaired_out1.fastqsolexa b/...immomatic_pe_r2_unpaired_out1.fastqsolexa → ...immomatic_pe_r2_unpaired_out1.fastqsolexa
diff --git a/...rimmomatic_pe_r2_unpaired_out1_clip.fastq → ...rimmomatic_pe_r2_unpaired_out1_clip.fastq b/...rimmomatic_pe_r2_unpaired_out1_clip.fastq → ...rimmomatic_pe_r2_unpaired_out1_clip.fastq
diff --git a/...momatic/test-data/trimmomatic_se_out1.err → ...momatic/test-data/trimmomatic_se_out1.err b/...momatic/test-data/trimmomatic_se_out1.err → ...momatic/test-data/trimmomatic_se_out1.err
diff --git a/...matic/test-data/trimmomatic_se_out1.fastq → ...matic/test-data/trimmomatic_se_out1.fastq b/...matic/test-data/trimmomatic_se_out1.fastq → ...matic/test-data/trimmomatic_se_out1.fastq
diff --git a/...ic/test-data/trimmomatic_se_out1.fastq.gz → ...ic/test-data/trimmomatic_se_out1.fastq.gz b/...ic/test-data/trimmomatic_se_out1.fastq.gz → ...ic/test-data/trimmomatic_se_out1.fastq.gz
diff --git a/...momatic/test-data/trimmomatic_se_out1.log → ...momatic/test-data/trimmomatic_se_out1.log b/...momatic/test-data/trimmomatic_se_out1.log → ...momatic/test-data/trimmomatic_se_out1.log
diff --git a/...momatic/test-data/trimmomatic_se_out2.err → ...momatic/test-data/trimmomatic_se_out2.err b/...momatic/test-data/trimmomatic_se_out2.err → ...momatic/test-data/trimmomatic_se_out2.err
diff --git a/...matic/test-data/trimmomatic_se_out2.fastq → ...matic/test-data/trimmomatic_se_out2.fastq b/...matic/test-data/trimmomatic_se_out2.fastq → ...matic/test-data/trimmomatic_se_out2.fastq
diff --git a/tools/trimmomatic/trimmomatic.xml → legacy/trimmomatic/trimmomatic.xml b/tools/trimmomatic/trimmomatic.xml → legacy/trimmomatic/trimmomatic.xml
diff --git a/tools/trimmomatic/trimmomatic_macros.xml → legacy/trimmomatic/trimmomatic_macros.xml b/tools/trimmomatic/trimmomatic_macros.xml → legacy/trimmomatic/trimmomatic_macros.xml