Mercurial > repos > galaxyp > mqppep_preproc
comparison 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 |
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| 0:8dfd5d2b5903 | 1:b76c75521d91 |
|---|---|
| 1 <macros> | 1 <macros> |
| 2 <token name="@TOOL_VERSION@">0.1.13</token> | 2 <token name="@TOOL_VERSION@">0.1.15</token> |
| 3 <token name="@VERSION_SUFFIX@">0</token> | 3 <token name="@VERSION_SUFFIX@">0</token> |
| 4 <xml name="requirements"> | 4 <xml name="requirements"> |
| 5 <requirements> | 5 <requirements> |
| 6 <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> | 6 <requirement type="package" version="1.56.0" >bioconductor-preprocesscore</requirement> |
| 7 <requirement type="package" version="1.22.2" >numpy</requirement> | 7 <requirement type="package" version="6.2.1" >gmp</requirement> |
| 8 <requirement type="package" version="1.23.4" >numpy</requirement> | |
| 8 <requirement type="package" version="0.3.3" >openblas</requirement> | 9 <requirement type="package" version="0.3.3" >openblas</requirement> |
| 9 <requirement type="package" version="1.4.1" >pandas</requirement> | 10 <requirement type="package" version="1.5.1" >pandas</requirement> |
| 10 <requirement type="package" version="1.64" >perl-dbd-sqlite</requirement> | 11 <requirement type="package" version="1.70" >perl-dbd-sqlite</requirement> |
| 11 <requirement type="package" version="5.26.2" >perl</requirement> | 12 <requirement type="package" version="5.32.1" >perl</requirement> |
| 12 <requirement type="package" version="1.4.0" >pyahocorasick</requirement> | 13 <requirement type="package" version="1.4.4" >pyahocorasick</requirement> |
| 13 <requirement type="package" version="3.9.10" >python</requirement> | 14 <requirement type="package" version="3.10.6" >python</requirement> |
| 14 <requirement type="package" version="1.14.2" >r-data.table</requirement> | 15 <requirement type="package" version="4.1.3" >r-base</requirement> |
| 15 <requirement type="package" version="1.1.2" >r-dbi</requirement> | 16 <requirement type="package" version="6.0_93" >r-caret</requirement> |
| 16 <requirement type="package" version="3.3.5" >r-ggplot2</requirement> | 17 <requirement type="package" version="1.14.4" >r-data.table</requirement> |
| 18 <requirement type="package" version="1.1.3" >r-dbi</requirement> | |
| 19 <requirement type="package" version="3.3.6" >r-ggplot2</requirement> | |
| 17 <requirement type="package" version="3.1.3" >r-gplots</requirement> | 20 <requirement type="package" version="3.1.3" >r-gplots</requirement> |
| 18 <requirement type="package" version="0.9.4" >r-latex2exp</requirement> | 21 <requirement type="package" version="0.9.5" >r-latex2exp</requirement> |
| 19 <requirement type="package" version="1.7.1" >r-optparse</requirement> | 22 <requirement type="package" version="1.7.3" >r-optparse</requirement> |
| 20 <requirement type="package" version="1.4.4" >r-reshape2</requirement> | 23 <requirement type="package" version="1.4.4" >r-reshape2</requirement> |
| 21 <requirement type="package" version="2.11" >r-rmarkdown</requirement> | 24 <requirement type="package" version="2.17" >r-rmarkdown</requirement> |
| 22 <requirement type="package" version="2.2.8" >r-rsqlite</requirement> | 25 <!-- |
| 23 <requirement type="package" version="0.4.0" >r-sass</requirement> | 26 <requirement type="package" version="2.2.18" >r-rsqlite</requirement> |
| 27 <requirement type="package" version="0.4.2" >r-sass</requirement> | |
| 28 --> | |
| 29 <requirement type="package" version="1.2.2" >r-sessioninfo</requirement> | |
| 24 <requirement type="package" version="0.4_11" >r-sqldf</requirement> | 30 <requirement type="package" version="0.4_11" >r-sqldf</requirement> |
| 25 <requirement type="package" version="1.4.0" >r-stringr</requirement> | 31 <requirement type="package" version="1.4.1" >r-stringr</requirement> |
| 26 <requirement type="package" version="0.37" >r-tinytex</requirement> | 32 <requirement type="package" version="0.42" >r-tinytex</requirement> |
| 27 <requirement type="package" version="0.3.7" >r-vioplot</requirement> | 33 <requirement type="package" version="0.3.7" >r-vioplot</requirement> |
| 28 <!-- | 34 <!-- |
| 29 It would be nice to use conda-forge/texlive-core rather than r-tinytex because the | 35 It would be nice to use conda-forge/texlive-core rather than r-tinytex because the |
| 30 former installs texlive when the package is built, but issue 23 blocked PDF-creation. | 36 former installs texlive when the package is built, but issue 19/61 blocked PDF-creation. |
| 31 Also, texlive-core also gave pango font errors (output had missing symbols replaced | 37 Also, texlive-core also gave pango font errors (output had missing symbols replaced |
| 32 with boxes) unless I specified the build as well as the version when building a | 38 with boxes) unless I specified the build as well as the version when building a |
| 33 conda environment, e.g.: texlive-core=20210325=h97429d4_0 | 39 conda environment, e.g.: texlive-core=20210325=h97429d4_0 |
| 34 --> | 40 --> |
| 35 </requirements> | 41 </requirements> |
| 36 <!-- 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): | 42 <!-- I specified the versions above because it takes a VERY long time |
| 37 echo n | time conda create -n mqppep_ver -c conda-forge -c bioconda \ | 43 to search for package versions when they are not omitted; also, |
| 38 bioconductor-preprocesscore=1.56.0 \ | 44 locking version numbers might lead to more-reproducible behavior. |
| 39 numpy=1.22.2 \ | |
| 40 openblas=0.3.3 \ | |
| 41 pandas=1.4.1 \ | |
| 42 perl-dbd-sqlite=1.64 \ | |
| 43 perl-dbd-sqlite=1.64 \ | |
| 44 perl=5.26.2 \ | |
| 45 pyahocorasick=1.4.0 \ | |
| 46 python=3.9.10 \ | |
| 47 r-data.table=1.14.2 \ | |
| 48 r-dbi=1.1.2 \ | |
| 49 r-ggplot2=3.3.5 \ | |
| 50 r-gplots=3.1.3 \ | |
| 51 r-latex2exp=0.9.4 \ | |
| 52 r-optparse=1.7.1 \ | |
| 53 r-reshape2=1.4.4 \ | |
| 54 r-rmarkdown=2.11 \ | |
| 55 r-rsqlite=2.2.8 \ | |
| 56 r-sass=0.4.0 \ | |
| 57 r-sqldf=0.4_11 \ | |
| 58 r-stringr=1.4.0 \ | |
| 59 r-tinytex=0.37 \ | |
| 60 r-vioplot=0.3.7 | |
| 61 with this (42 or more seconds): | |
| 62 echo n | time conda create -n mqppep_nover -c conda-forge -c bioconda \ | |
| 63 bioconductor-preprocesscore= \ | |
| 64 numpy \ | |
| 65 openblas=0.3.3 \ | |
| 66 pandas \ | |
| 67 perl \ | |
| 68 perl-dbd-sqlite \ | |
| 69 perl-dbd-sqlite \ | |
| 70 pyahocorasick \ | |
| 71 python \ | |
| 72 r-data.table \ | |
| 73 r-dbi \ | |
| 74 r-ggplot2 \ | |
| 75 r-gplots \ | |
| 76 r-latex2exp \ | |
| 77 r-optparse \ | |
| 78 r-reshape2 \ | |
| 79 r-rmarkdown \ | |
| 80 r-rsqlite \ | |
| 81 r-sass \ | |
| 82 r-sqldf \ | |
| 83 r-stringr \ | |
| 84 r-tinytex \ | |
| 85 r-vioplot | |
| 86 | |
| 87 --> | 45 --> |
| 88 </xml> | 46 </xml> |
| 89 </macros> | 47 </macros> |