[ci skip] Merge PR 33600

Merge PR bioconda#33600, commits were: * Update meta.yaml * Merge branch 'master' into update_vsclust * Merge branch 'master' into update_vsclust * Merge branch 'master' into update_vsclust * fixed bioconductor * fixed bioconductor * Update build-fail-blacklist * Merge branch 'master' into update_vsclust * updated vsclust * update test * Merge branch 'update_vsclust' of github.com:veitveit/bioconda-recipes into update_vsclust * first test * Merge pull request #1 from veitveit/master updating * first test * Merge branch 'master' into maxquant-patch-2 * downgraded mono * changed to mono * changed to mono * changed to mono * corrected version * corrected version * Merge branch 'maxquant-patch-2' of https://github.com/veitveit/bioconda-recipes into maxquant-patch-2 * Merge branch 'bioconda:master' into maxquant-patch-2 * testing * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update maxquant dependency on dotnet MaxQuant needs a newer version of dotnet. Probably due to a versioning problem with libssl (not sure).
nextstrain · Mar 29, 2022 · 41a5a66 · 41a5a66
1 parent ea04ba3
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -16,7 +16,6 @@ recipes/mockinbird
 recipes/sparse-neighbors-search
 recipes/msaprobs
 recipes/mgkit
-recipes/vsclust
 recipes/starseqr
 recipes/desman
 recipes/sqt

diff --git a/recipes/vsclust/build.sh b/recipes/vsclust/build.sh
@@ -5,22 +5,26 @@ mkdir -p $PREFIX/lib/R/library/e1071FuzzVec
 R CMD INSTALL --build e1071FuzzVec_Installation
 cp -r e1071FuzzVec_Installation/* $PREFIX/lib/R/library/e1071FuzzVec/
 
+
 # move all files to outdir and link into it by bin executor
 mkdir -p $PREFIX/bin
 mkdir -p $PREFIX/share/vsclust
 # substituting paths for testing 
-cp run_app_conda.R run_vsclust_app.R
+sed -i'.orig' "s=HelperFuncs.R=../share/vsclust/HelperFuncs.R=" runVSClust.R
 sed -i'.orig' "s=FcmClustPEst.R=../share/vsclust/FcmClustPEst.R=" runVSClust.R
 sed -i'.orig' "s=mfuzz.plotpdf.R=../share/vsclust/mfuzz.plotpdf.R=" runVSClust.R
-sed -i'.orig' "s=HelperFuncs.R=../share/vsclust/HelperFuncs.R=" runVSClust.R
-echo "after sed"
+
+
+
+# copying files
 cp *.R $PREFIX/share/vsclust/
 cp ProtExample.csv $PREFIX/share/vsclust/
 cp vsclust.yml $PREFIX/share/vsclust/
 cp runVSClust.R $PREFIX/bin
 cp run_vsclust_app.R $PREFIX/bin
-echo "before chmod"
+
+
+# move all files to outdir and link into it by bin executor
 chmod a+x $PREFIX/bin/runVSClust.R
 chmod a+x $PREFIX/bin/run_vsclust_app.R
 
-
diff --git a/recipes/vsclust/meta.yaml b/recipes/vsclust/meta.yaml
@@ -1,67 +1,62 @@
 {% set name = "VSClust" %}
-{% set version = "0.87" %}
+{% set version = "0.91" %}
+{% set bioc = "3.14" %}
 
 package:
   name: vsclust
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
+  noarch: generic
   rpaths:
     - lib/R/lib/
     - lib/
 
 source:
-  url: https://bitbucket.org/veitveit/vsclust/get/release-{{ version }}.tar.gz
-  sha256: cf00b1c43e77dd2e1c3779932537613ac00b44173c231393eb54a86a334ca542
+  url: https://bitbucket.org/veitveit/vsclust/get/release-0.91.tar.gz
+  sha256: 23b6b699a5abeb04d12c9a7e01e9b85de62d684fc1c1cb4315861c215e0a68a4
 
 requirements:
-  build:
-    - {{ compiler('cxx') }}
-    - {{ compiler('fortran') }}
   host:
-    - r-base 3.6.3
-    - r-matrixstats >=0.56
-    - bioconductor-mfuzz >=2.46.0
-    - bioconductor-qvalue >=2.16.0
-    - bioconductor-limma
+     - r-base
+     - r-matrixstats
+     - bioconductor-mfuzz
+     - bioconductor-qvalue
+     - bioconductor-limma
   run:
-    - r-base 3.6.3
-    - r-matrixstats >=0.56.0
-    - r-dt
-    - bioconductor-mfuzz >=2.46.0
-    - bioconductor-qvalue >=2.16.0
-    - bioconductor-limma
-    - bioconductor-clusterprofiler
-    - bioconductor-RDAVIDWebService
-    - r-readxl >=1.3.1
-    - r-shiny >=1.4.0
-    - r-yaml >=2.2.0
-    - r-shinyjs >=1.1
-    - r-shinythemes >=1.1.2
-    - r-data.table >=1.12.8
-    - r-stringi
+    - r-parallelly
+    - r-base
+    - r-matrixstats
+    - bioconductor-mfuzz
+    - bioconductor-qvalue
+    - bioconductor-limma 
+    - bioconductor-clusterprofiler 4.2.0
+#    - bioconductor-RDAVIDWebService
+    - r-readxl
+#    - r-shiny 1.7.1
+    - r-yaml 
+    - r-shinyjs
+    - r-shinythemes
+    - r-data.table
 
 test:
   commands:
-     - cp $PREFIX/share/vsclust/ProtExample.csv .; runVSClust.R $PREFIX/share/vsclust/vsclust.yml
+     -  cp $PREFIX/share/vsclust/ProtExample.csv .; runVSClust.R $PREFIX/share/vsclust/vsclust.yml
 
 about:
   home: https://bitbucket.org/veitveit/vsclust/src/master/
   license: 'GPL (>=2)'
   license_family: GPL
   license_file: LICENSE
-  summary: "Interactive tool for statistical testing, data browsing and interactive visualizationc of quantitative omics data"
-  description: | 
-        VSClust is a web service (shiny app) and command-line tool for statistical testing, 
-        clustering and interactive visualization of quantitative omics data. Its 
-        variance-sensitive clustering algorithm improves identification of co-regulated 
-        features in noisy data with replicates
+  summary: Interactive tool for statistical testing, data browsing and interactive visualization of quantitative omics data
+  description: |
+    VSClust is a web service (shiny app) and command-line tool for statistical testing, clustering and interactive visualization of quantitative omics data. Its variance-sensitive clustering algorithm improves identification of co-regulated features in noisy data with replicates
 
 extra:
-  notes: | 
-        The shiny app can be run with the run_vsclust_app.sh command. Alternatively, 
-        a command-line version is available: runVSClust.R
+  notes: |
+    The shiny app can be run with the run_app.sh command. Alternative, a command-line version is available: runVSClust.R
   identifiers:
     - biotools:vsclust
     - doi:10.1093/bioinformatics/bty224 
+