fix tools failing ci

cummerbund: fix requirements - 2.16.0 was not installable anymore (conda took forever) 2.20 was the closest that worked. I added r-base to speed up conda. - added fonts for pngs that actually contain text - removed unneeded r-png requirement - switch from test data to asserts cufflinks: - moved to IUC galaxyproject/tools-iuc#3069 dwt*: - remove perl wrappers and use Rscripts directly Co-authored-by: Nicola Soranzo <[email protected]>
galaxyproject · Jul 1, 2020 · 4e17a8d · 4e17a8d
1 parent 7907a6b
commit 4e17a8d
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diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -203,7 +203,7 @@ jobs:
     - name: lintr
       run: |
         library(lintr)
-        linters <- with_defaults(line_length_linter = NULL)
+        linters <- with_defaults(line_length_linter = NULL, cyclocomp_linter = NULL)
         con <- file("../workflow_artifacts/changed_repositories.list", "r")
         status <- 0
         while (TRUE) {

diff --git a/.tt_skip b/.tt_skip
@@ -36,10 +36,6 @@ tools/dgidb_annotator
 tools/divide_pg_snp
 tools/dna_filtering
 tools/draw_stacked_barplots
-tools/dwt_cor_ava_perclass
-tools/dwt_cor_avb_all
-tools/dwt_ivc_all
-tools/dwt_var_perclass
 tools/express
 tools/fastqsolexa_to_fasta_qual
 tools/featurecounter

diff --git a/tool_collections/cufflinks/cuff_macros.xml b/tool_collections/cufflinks/cuff_macros.xml
diff --git a/tool_collections/cufflinks/cuffcompare/.shed.yml b/tool_collections/cufflinks/cuffcompare/.shed.yml
diff --git a/tool_collections/cufflinks/cuffcompare/cuff_macros.xml b/tool_collections/cufflinks/cuffcompare/cuff_macros.xml
diff --git a/tool_collections/cufflinks/cuffcompare/cuffcompare_wrapper.py b/tool_collections/cufflinks/cuffcompare/cuffcompare_wrapper.py