ceuadmin
The CEU software repository is here, /usr/local/Cluster-Apps/ceuadmin/. The current list is as follows,
[1] "ABCtoolbox" "akt" "alpine"
[4] "annovar" "aria2" "axel"
[7] "bazel" "bcftools" "Beagle"
[10] "bedops" "bedtools2" "bgen"
[13] "biobank" "blat" "boltlmm"
[16] "brotli" "CaVEMaN" "CAVIAR"
[19] "CAVIARBF" "ccal" "circos"
[22] "citeproc" "cppunit" "crossmap"
[25] "Cytoscape" "DEPICT" "DjVuLibre"
[28] "docbook2X" "DosageConverter" "Eagle"
[31] "ensembl-vep" "exiv2" "exomeplus"
[34] "expat" "FastQTL" "fcGENE"
[37] "ffmpeg" "fgwas" "finemap"
[40] "fossil" "fribidi" "GARFIELD"
[43] "gcta" "gdal" "GEM"
[46] "GEMMA" "Genotype-Harmonizer" "gettext"
[49] "ghc" "ghostscript" "git"
[52] "git-extras" "GitKraken" "gmp"
[55] "gnutls" "googletest" "GraphicsMagick"
[58] "GreenAlgorithms4HPC" "gtksourceview" "gtool"
[61] "hpg" "htslib" "icu"
[64] "impute" "JAGS" "jq"
[67] "KentUtils" "KING" "lapack"
[70] "ldc2" "LDstore" "LEMMA"
[73] "libcares" "libgit2" "libglvnd"
[76] "libiconv" "libidn2" "libntlm"
[79] "libpng" "libsodium" "libssh2"
[82] "libuv" "libxml2" "libxslt"
[85] "locuszoom" "MAGENTA" "magma"
[88] "MAGMA" "Mega2" "metal"
[91] "MONSTER" "MORGAN" "MR-MEGA"
[94] "MsCAVIAR" "nano" "ncurses"
[97] "netbeans" "nettle" "NLopt"
[100] "node" "nspr" "oniguruma"
[103] "OpenMS" "openssl" "osca"
[106] "PAINTOR" "pandoc" "pandoc-citeproc"
[109] "parallel" "Pascal" "pcre2"
[112] "pdf2djvu" "phenoscanner" "plink"
[115] "plink-bgi" "plinkseq" "polyphen"
[118] "poppler" "proj" "PRSice"
[121] "pspp" "qctool" "qpdf"
[124] "qt" "qtcreator" "QTLtools"
[127] "quicktest" "R" "raremetal"
[130] "rclone" "readline" "regenie"
[133] "rstudio" "ruby" "samtools"
[136] "shapeit" "SMR" "snakemake"
[139] "SNP2HLA" "snptest" "sqlite"
[142] "ssw" "STAR" "stata"
[145] "SurvivalAnalysis" "SurvivalKit" "tabix"
[148] "tidy" "trinculo" "trousers"
[151] "Typora" "unbound" "vala"
[154] "vcftools" "VEGAS2" "VSCode"
[157] "yaml-cpp" "zstd"
These are wrapped up as modules
.
The module files are defined at /usr/local/Cluster-Config/modulefiles/ceuadmin. Most software use gcc/6; when required it can be enabled with module load gcc/6
.
Most should be available to all CSD3 users at the campus, e.g., for pspp, a brief description of a module is available with
module help ceuadmin/pspp
and the module is loaded and graphical user interface (GUI)1 started with
module load ceuadmin/pspp
psppire
for PSPP 1.6.0. Once the job is done, one can restore the previous environment with
module unload ceuadmin/pspp
A full list of module subcommands is available with module help
as detailed here for
3.2.9 – CSD3 uses version 3.2.10 dated 2012-12-21. In particular, module whatis ceuadmin/ensembl-vep
indicates usage regarding build37/build38 setup for the loftee
plugin used in loss of function (LoF)
annotation.
Ideally, software with large size / reference data will be available from /rds/project/jmmh2/software. However, CEU users will be able to use ANNOVAR, ensembl-vep, OpenMS, polyphen, KentUtils/MAGMA/Pascal/VEGASV2/fgwas/locuszoom linking internal projects/personal space (additional requests need to be made). Further information is avaiiable from doc/ceuadmin.md, ceuadmin.html. A large collection of R packages (1,258 as of November 2022) is linked with ceuadmin/R/4.2.2, the latest R distribution, please drop an email to jhz22@medschl.cam.ac.uk for access. The original list prior to mid-November 2022 is given below2.
-
GUI
As GUI-based programs claim more computing resources, it is recommended that they are only used occasionally, e.g., calling back GitHub sessions. ↩
-
The original list was a mixture of modules and directories as follows,
bgenix/ impute_v2.3.2_x86_64_static/ plink/ R/ Raremetal_linux_executables/ snptest_new/ biobank/ interval/ plink_1.90_beta/ raremetal_4.13/ Raremetal_linux_executables.tgz source/ boltlmm/ JAGS/ plink_bgi_Dev/ raremetal_4.13.3/ raremetal.log stata/ boltlmm_2.2/ LDstore/ plink-bgi_linux_x86_64_may/ raremetal_4.13.4/ regenie/ tabix/ crossmap/ locuszoom/ plink_linux_x86_64_beta2a/ raremetal_4.13.5/ samtools-1.10.tar.bz2 temp/ exomeplus/ magma/ plink_linux_x86_64_beta3.32/ raremetal_4.13.7/ samtools_1.2/ vcftools/ gcta/ MAGMA_Celltyping/ plinkseq-0.08-x86_64/ raremetal_4.13.8/ shapeit.v2.r790.RHELS_5.4.dynamic/ vcftools_ps629/ gtool_v0.7.5_x86_64/ metabolomics/ plinkseq-0.10/ raremetal_4.14.0/ snptest/ hpg/ metal/ pspp/ raremetal_4.14.1/ snptest_2.5.2/ htslib/ metal_updated/ qctool_v1.4-linux-x86_64/ raremetal_BPGen/ snptest_2.5.4_beta3/
A grep of recent add-ons in the Genetics category is as follows,
Date Add.ons Category 2022-10-22 snptest/2.5.6 Genetics "" qctool/2.0.8 Genetics "" gcta/1.94.1 Genetics "" KING/2.1.6 Genetics "" LDstore/2.0 Genetics "" shapeit/3 Genetics "" vcftools/0.1.16 Genetics "" finemap/1.4 Genetics 2022-10-23 quicktest/1.1 Genetics "" samtools/1.11 Genetics "" bcftools/1.12 Genetics "" MORGAN/3.4 Genetics "" METAL/2020-05-05r Genetics3 "" regenie/3.2.1 Genetics "" GEMMA/0.98.5 Genetics4 "" htslib/1.12 Genetics "" fcGENE/1.0.7 Genetics5 "" SMR/1.0.3 Genetics "" FastQTL/2.165 Genetics 2022-10-26 circos/0.69-9 Genetics "" bgen/1.1.7 Genetics "" DosageConverter/1.0.0 Genetics "" QTLtools/1.3.1-25 Genetics6 "" blat/37x1 Genetics "" bedtools2/2.29.2 Genetics "" bedops/2.4.41 Genetics 2022-11-03 Beagle/3.0.4 Genetics 2022-11-08 CrossMap/0.6.4 Genetics "" SurvivalKit/6.12 Genetics "" PRSice/2.3.3 Genetics 2022-11-09 qctool/2.2.0 Genetics 2022-11-10 CaVEMaN/1.01-c1815a0 Genetics "" akt/0.3.3 Genetics "" MsCAVIAR/0.6.4 Genetics "" CAVIAR/2.2 Genetics "" MONSTER/1.3 Genetics "" osca/0.46 Genetics "" LEMMA/1.0.4 Genetics7 "" CAVIARBF/0.2.1 Genetics 2022-11-11 PAINTOR/3.0 Genetics 2022-11-14 MR-MEGA/0.2 Genetics 2022-11-16 SNP2HLA/1.0.3 Genetics "" STAR/2.7.10b Genetics "" Mega2/6.0.0 Genetics 2022-11-19 ensembl-vep/104 Genetics* "" OpenMS/3.0.0 Genetics*8 "" polyphen/2.2.2 Genetics* "" ANNOVAR/24Oct2019 Genetics* "" MAGENTA/vs2_July2011 Genetics* "" GARFIELD/v2 Genetics* "" KentUtils/2022-11-14 Genetics* 2022-11-20 Genotype-Harmonizer/1.4.25 Genetics 2022-11-21 locuszoom/1.4 Genetics*9 "" DEPICT/v1_rel194 Genetics* "" MAGMA/1.10 Genetics* "" Pascal/v_debut Genetics* "" VEGAS2/2.01.17 Genetics* "" fgwas/0.3.6 Genetics* 2022-12-04 phenoscanner/v2 Genetics* 2022-12-07 SurvivalAnalysis/2016-05-09 Genetics 2023-01-03 Eagle/2.4.1 Genetics 2023-01-05 GEM/1.4.5 Genetics * CEU or approved users only. ↩
-
Notes on METAL 2020-05-05r
This version has options EFFECT_PRINT_PRECISION and STDERR_PRINT_PRECISION (both with default 4) to enable many decimal places.
The letter
r
as in2020-05-05r
indicates a replacement of functions inlibsrc/MathStats.cpp
to ensure generality – details have also been posted to the GitHub page, https://github.com/statgen/METAL/issues/24.FATAL ERROR - a too large, ITMAX too small in gamma countinued fraction (gcf) so the -1.info file could not be generated.
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Note on compiling from source
A considerably smaller (1,097,256 vs 22,721,624) executable, /usr/local/Cluster-Apps/ceuadmin/GEMMA/0.98.5/bin, is generated under CSD3 but the original distribution is used by default.
module load openblas/0.2.15 make
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Alternative site
-
The long version number is 1.3.1-25-g6e49f85f20. ↩
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The documentation indicates a requirement of gcc/9.4, boost/1.78, OpenMP/3.1 and/or Intel MKL Library 2019 Update 1 but it is possible to proceed with gcc/11, cmake-3.19.7-gcc-5.4-5gbsejo, boost-1.66.0-gcc-5.4.0-slpq3un, ceuadmin/bgen/1.1.7. ↩
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When the OpenMS module is loaded, pyopenms and alphapept also become available. ↩
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locuszoom
The version adds chromosome X data and will have options using INTERVAL data. ↩