diff macros.xml @ 1:b76c75521d91 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
author galaxyp
date Fri, 28 Oct 2022 18:26:42 +0000
parents 8dfd5d2b5903
children a5e7469dfdfa
line wrap: on
line diff
--- a/macros.xml	Mon Jul 11 19:22:54 2022 +0000
+++ b/macros.xml	Fri Oct 28 18:26:42 2022 +0000
@@ -1,89 +1,47 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.1.13</token>
+    <token name="@TOOL_VERSION@">0.1.15</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.56.0"  >bioconductor-preprocesscore</requirement>
-            <requirement type="package" version="1.22.2"  >numpy</requirement>
+            <requirement type="package" version="6.2.1"   >gmp</requirement>
+            <requirement type="package" version="1.23.4"  >numpy</requirement>
             <requirement type="package" version="0.3.3"   >openblas</requirement>
-            <requirement type="package" version="1.4.1"   >pandas</requirement>
-            <requirement type="package" version="1.64"    >perl-dbd-sqlite</requirement>
-            <requirement type="package" version="5.26.2"  >perl</requirement>
-            <requirement type="package" version="1.4.0"   >pyahocorasick</requirement>
-            <requirement type="package" version="3.9.10"  >python</requirement>
-            <requirement type="package" version="1.14.2"  >r-data.table</requirement>
-            <requirement type="package" version="1.1.2"   >r-dbi</requirement>
-            <requirement type="package" version="3.3.5"   >r-ggplot2</requirement>
+            <requirement type="package" version="1.5.1"   >pandas</requirement>
+            <requirement type="package" version="1.70"    >perl-dbd-sqlite</requirement>
+            <requirement type="package" version="5.32.1"  >perl</requirement>
+            <requirement type="package" version="1.4.4"   >pyahocorasick</requirement>
+            <requirement type="package" version="3.10.6"  >python</requirement>
+            <requirement type="package" version="4.1.3"   >r-base</requirement>
+            <requirement type="package" version="6.0_93"  >r-caret</requirement>
+            <requirement type="package" version="1.14.4"  >r-data.table</requirement>
+            <requirement type="package" version="1.1.3"   >r-dbi</requirement>
+            <requirement type="package" version="3.3.6"   >r-ggplot2</requirement>
             <requirement type="package" version="3.1.3"   >r-gplots</requirement>
-            <requirement type="package" version="0.9.4"   >r-latex2exp</requirement>
-            <requirement type="package" version="1.7.1"   >r-optparse</requirement>
+            <requirement type="package" version="0.9.5"   >r-latex2exp</requirement>
+            <requirement type="package" version="1.7.3"   >r-optparse</requirement>
             <requirement type="package" version="1.4.4"   >r-reshape2</requirement>
-            <requirement type="package" version="2.11"    >r-rmarkdown</requirement>
-            <requirement type="package" version="2.2.8"   >r-rsqlite</requirement>
-            <requirement type="package" version="0.4.0"   >r-sass</requirement>
+            <requirement type="package" version="2.17"    >r-rmarkdown</requirement>
+            <!--
+            <requirement type="package" version="2.2.18"  >r-rsqlite</requirement>
+            <requirement type="package" version="0.4.2"   >r-sass</requirement>
+            -->
+            <requirement type="package" version="1.2.2"   >r-sessioninfo</requirement>
             <requirement type="package" version="0.4_11"  >r-sqldf</requirement>
-            <requirement type="package" version="1.4.0"   >r-stringr</requirement>
-            <requirement type="package" version="0.37"    >r-tinytex</requirement>
+            <requirement type="package" version="1.4.1"   >r-stringr</requirement>
+            <requirement type="package" version="0.42"    >r-tinytex</requirement>
             <requirement type="package" version="0.3.7"   >r-vioplot</requirement>
             <!--
             It would be nice to use conda-forge/texlive-core rather than r-tinytex because the
-            former installs texlive when the package is built, but issue 23 blocked PDF-creation.
+            former installs texlive when the package is built, but issue 19/61 blocked PDF-creation.
             Also, texlive-core also gave pango font errors (output had missing symbols replaced
             with boxes) unless I specified the build as well as the version when building a
             conda environment, e.g.:  texlive-core=20210325=h97429d4_0
             -->
         </requirements>
-        <!-- I specified the versions above because it takes a VERY long time to search for package versions when they are not omitted; also, version numbers should lead to reproducible behavior.  Contrast execution times of this (about 18 seconds):
-            echo n | time conda create -n mqppep_ver -c conda-forge -c bioconda \
-              bioconductor-preprocesscore=1.56.0 \
-              numpy=1.22.2 \
-              openblas=0.3.3 \
-              pandas=1.4.1 \
-              perl-dbd-sqlite=1.64 \
-              perl-dbd-sqlite=1.64 \
-              perl=5.26.2 \
-              pyahocorasick=1.4.0 \
-              python=3.9.10 \
-              r-data.table=1.14.2 \
-              r-dbi=1.1.2 \
-              r-ggplot2=3.3.5 \
-              r-gplots=3.1.3 \
-              r-latex2exp=0.9.4 \
-              r-optparse=1.7.1 \
-              r-reshape2=1.4.4 \
-              r-rmarkdown=2.11 \
-              r-rsqlite=2.2.8 \
-              r-sass=0.4.0 \
-              r-sqldf=0.4_11 \
-              r-stringr=1.4.0 \
-              r-tinytex=0.37 \
-              r-vioplot=0.3.7
-          with this (42 or more seconds):
-            echo n | time conda create -n mqppep_nover -c conda-forge -c bioconda \
-              bioconductor-preprocesscore= \
-              numpy \
-              openblas=0.3.3 \
-              pandas \
-              perl \
-              perl-dbd-sqlite \
-              perl-dbd-sqlite \
-              pyahocorasick \
-              python \
-              r-data.table \
-              r-dbi \
-              r-ggplot2 \
-              r-gplots \
-              r-latex2exp \
-              r-optparse \
-              r-reshape2 \
-              r-rmarkdown \
-              r-rsqlite \
-              r-sass \
-              r-sqldf \
-              r-stringr \
-              r-tinytex \
-              r-vioplot
-
+        <!-- I specified the versions above because it takes a VERY long time
+             to search for package versions when they are not omitted; also,
+             locking version numbers might lead to more-reproducible behavior.
         -->
     </xml>
 </macros>