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@jinghuazhao
jinghuazhao committed Apr 29, 2024
1 parent a27a1fe commit 6b290e7
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2 changes: 1 addition & 1 deletion R/jqr.md
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Expand Up @@ -72,7 +72,7 @@ rm jqr_*
This mirrors efforts above.

```bash
# download.packages("jqr",".")
# Rscript -e 'download.packages("jqr",".")'
tar xvfz jqr_1.3.3.tar.gz
cd jqr
mv configure configure.sav
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27 changes: 27 additions & 0 deletions R/magick.md
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Expand Up @@ -6,6 +6,8 @@ sort: 12

> The magick package provide a modern and simple toolkit for image processing in R. It wraps the ImageMagick STL which is the most comprehensive open-source image processing library available today.
## 2.7.1

When installing the package we have error message,

```
Expand Down Expand Up @@ -60,3 +62,28 @@ it turned out that the required ImageMick needs to be loaded as follows,
```bash
module load image-magick-7.0.5-9-gcc-5.4.0-d4lemcc
```

## 2.8.3

It turned out gcc/6 is required for module `image-magick-7.0.5-9-gcc-5.4.0-d4lemcc`, coupling with C++11 via ~/.R/Makevars.

```
CC=gcc
CXX=g++ -std=gnu++11
PKG_CXXFLAGS= -std=c++11
CFLAGS = -std=c99 -I/usr/include -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-deprecated-declarations -Wno-parentheses -Wimplicit-function-declaration
CXXFLAGS = -std=c++11
```

The setup is appropriate for module `ceuadmin/ImageMagick/7.1.1-31` with `src/Makevars` and a disabled `configure`,

```
PKG_CPPFLAGS=-fopenmp -DMAGICKCORE_HDRI_ENABLE=1 -DMAGICKCORE_QUANTUM_DEPTH=16 -DMAGICKCORE_CHANNEL_MASK_DEPTH=32 -I/usr/local/Cluster-Apps/ceuadmin/ImageMagick/7.1.1-31/include/ImageMagick-7
PKG_CXXFLAGS=$(C_VISIBILITY)
PKG_LIBS=-L/usr/local/Cluster-Apps/ceuadmin/ImageMagick/7.1.1-31/lib -lm -lMagick++-7.Q16HDRI -lMagickWand-7.Q16HDRI -lMagickCore-7.Q16HDRI
all:
clean:
rm -f $(SHLIB) $(OBJECTS)
```
71 changes: 36 additions & 35 deletions systems/ceuadmin.md
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Expand Up @@ -8,7 +8,7 @@ The CEU software repository is here, **/usr/local/Cluster-Apps/ceuadmin/**.

![ceuadmin](ceuadmin.png)

noting that the importance of software is purely random according to $$Poisson(N,\lambda)$$ where $$N=223$$, $$\lambda=3$$.
noting that the importance of software is purely random according to $$Poisson(N,\lambda)$$ where $$N=225$$, $$\lambda=3$$.

## Entries

Expand Down Expand Up @@ -37,40 +37,41 @@ The current list is as follows,
[77] "googletest" "graphene" "GraphicsMagick" "GreenAlgorithms4HPC"
[81] "gsl" "gtk+" "gtksourceview" "gtool"
[85] "hpg" "htslib" "hunspell" "icu"
[89] "ImageJ" "impute" "JabRef" "JAGS"
[93] "jq" "json-c" "KentUtils" "KING"
[97] "krb5" "lapack" "ldc2" "ldsc"
[101] "LDstore" "LEMMA" "libcares" "libgit2"
[105] "libglvnd" "libiconv" "libidn2" "libntlm"
[109] "libpng" "libseccomp" "libsodium" "libssh"
[113] "libssh2" "libuv" "libxml2" "libxslt"
[117] "locuszoom" "LVM2" "MAGENTA" "magma"
[121] "Mango" "Mega2" "metal" "MONSTER"
[125] "MORGAN" "MR-MEGA" "MsCAVIAR" "nano"
[129] "ncbi-vdb" "ncurses" "netbeans" "nettle"
[133] "nextflow" "NLopt" "node" "nspr"
[137] "oniguruma" "openjdk" "OpenMS" "openssh"
[141] "openssl" "osca" "PAINTOR" "pandoc"
[145] "pandoc-citeproc" "pango" "parallel" "Pascal"
[149] "pcre2" "pdf2djvu" "pdfjam" "peer"
[153] "pgsc_calc" "phenoscanner" "PhySO" "picard"
[157] "plink" "plink-bgi" "plinkseq" "PoGo"
[161] "polyphen" "poppler" "popt" "proj"
[165] "PRSice" "pspp" "pulsar" "PWCoCo"
[169] "qctool" "qpdf" "qt" "qtcreator"
[173] "QTLtools" "quarto" "quicktest" "R"
[177] "raremetal" "rclone" "readline" "regenie"
[181] "regtools" "RHHsoftware" "rst2pdf" "rstudio"
[185] "ruby" "rust" "samtools" "Scala"
[189] "shapeit" "singularity" "SMR" "snakemake"
[193] "SNP2HLA" "snptest" "spread-sheet-widget" "sqlite"
[197] "sra-tools" "ssw" "STAR" "stata"
[201] "SurvivalAnalysis" "SurvivalKit" "Swift" "tabix"
[205] "tatami" "thunderbird" "tidy" "trinculo"
[209] "trousers" "Typora" "unbound" "vala"
[213] "VarScan" "vcftools" "VEGAS2" "verifyBamID"
[217] "VSCode" "VSCodium" "vte" "xpdf"
[221] "yaml-cpp" "Zotero" "zstd"
[89] "ImageJ" "ImageMagick" "impute" "JabRef"
[93] "JAGS" "jq" "json-c" "KentUtils"
[97] "KING" "krb5" "lapack" "ldc2"
[101] "ldsc" "LDstore" "LEMMA" "libcares"
[105] "libgit2" "libglvnd" "libiconv" "libidn2"
[109] "libntlm" "libpng" "libseccomp" "libsodium"
[113] "libssh" "libssh2" "libuv" "libxml2"
[117] "libxslt" "locuszoom" "LVM2" "MAGENTA"
[121] "magma" "Mango" "Mega2" "metal"
[125] "MONSTER" "MORGAN" "MR-MEGA" "MsCAVIAR"
[129] "nano" "ncbi-vdb" "ncurses" "netbeans"
[133] "nettle" "nextflow" "nlopt" "NLopt"
[137] "node" "nspr" "oniguruma" "openjdk"
[141] "OpenMS" "openssh" "openssl" "osca"
[145] "PAINTOR" "pandoc" "pandoc-citeproc" "pango"
[149] "parallel" "Pascal" "pcre2" "pdf2djvu"
[153] "pdfjam" "peer" "pgsc_calc" "phenoscanner"
[157] "PhySO" "picard" "plink" "plink-bgi"
[161] "plinkseq" "PoGo" "polyphen" "poppler"
[165] "popt" "proj" "PRSice" "pspp"
[169] "pulsar" "PWCoCo" "qctool" "qpdf"
[173] "qt" "qtcreator" "QTLtools" "quarto"
[177] "quicktest" "R" "raremetal" "rclone"
[181] "readline" "regenie" "regtools" "RHHsoftware"
[185] "rst2pdf" "rstudio" "ruby" "rust"
[189] "samtools" "Scala" "shapeit" "singularity"
[193] "SMR" "snakemake" "SNP2HLA" "snptest"
[197] "spread-sheet-widget" "sqlite" "sra-tools" "ssw"
[201] "STAR" "stata" "SurvivalAnalysis" "SurvivalKit"
[205] "Swift" "tabix" "tatami" "thunderbird"
[209] "tidy" "trinculo" "trousers" "Typora"
[213] "unbound" "vala" "VarScan" "vcftools"
[217] "VEGAS2" "verifyBamID" "VSCode" "VSCodium"
[221] "vte" "xpdf" "yaml-cpp" "Zotero"
[225] "zstd"
```

These are wrapped up as :star::star::star: **[modules](https://modules.readthedocs.io/en/latest/index.html)** :star::star::star:.
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14 changes: 13 additions & 1 deletion systems/setup.md
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Expand Up @@ -268,6 +268,7 @@ All entries are ordered chronologically.
! "" | libssh2/1.11.0-icelake | Generic |
! "" | libssh/0.10.6-icelake | Generic |
! 2024-04-22 | peer/1.3 | Generic[^peer] |
! 2024-04-29 | ImageMagick/7.1.1-31 | Generic[^ImageMagick]|

\* CEU or approved users only.

Expand All @@ -285,7 +286,7 @@ They are generated from the following script,
if [ "$(uname -n | sed 's/-[0-9]*$//')" == "login-p" ]; then
module load ceuadmin/R
else
module load ceuadmin/R/4.3.3-icelake
module load ceuadmin/R/4.4.0-icelake
fi
grep -e Generic ${CEUADMIN}/doc/setup.md | grep "^[|]" | awk '{print $4}' > generic.lst
grep -e Genetics ${CEUADMIN}/doc/setup.md | grep "^[|]" | awk '{print $4}' > genetics.lst
Expand Down Expand Up @@ -904,3 +905,14 @@ Rscript -e '
[^peer]: **peer**

This is documented separately in the R section, <https://cambridge-ceu.github.io/csd3/applications/peer.html>.

[^ImageMagick]: **ImageMagick**

```bash
wget -qO- https://github.com/ImageMagick/ImageMagick/archive/refs/tags/7.1.1-31.tar.gz | \
tar xvfz -
cd ImageMagick-7.1.1-31/
./configure --prefix=$CEUADMIN/ImageMagick/7.1.1-31
make
make install
```

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