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jinghuazhao committed Apr 22, 2024
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62 changes: 41 additions & 21 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 $$N=222$$, $$\lambda=3$$.
noting that the importance of software is purely random according to $$Poisson(N,\lambda)$$ where $$N=223$$, $$\lambda=3$$.

## Entries

Expand Down Expand Up @@ -52,25 +52,25 @@ The current list is as follows,
[137] "oniguruma" "openjdk" "OpenMS" "openssh"
[141] "openssl" "osca" "PAINTOR" "pandoc"
[145] "pandoc-citeproc" "pango" "parallel" "Pascal"
[149] "pcre2" "pdf2djvu" "pdfjam" "pgsc_calc"
[153] "phenoscanner" "PhySO" "picard" "plink"
[157] "plink-bgi" "plinkseq" "PoGo" "polyphen"
[161] "poppler" "popt" "proj" "PRSice"
[165] "pspp" "pulsar" "PWCoCo" "qctool"
[169] "qpdf" "qt" "qtcreator" "QTLtools"
[173] "quarto" "quicktest" "R" "raremetal"
[177] "rclone" "readline" "regenie" "regtools"
[181] "RHHsoftware" "rst2pdf" "rstudio" "ruby"
[185] "rust" "samtools" "Scala" "shapeit"
[189] "singularity" "SMR" "snakemake" "SNP2HLA"
[193] "snptest" "spread-sheet-widget" "sqlite" "sra-tools"
[197] "ssw" "STAR" "stata" "SurvivalAnalysis"
[201] "SurvivalKit" "Swift" "tabix" "tatami"
[205] "thunderbird" "tidy" "trinculo" "trousers"
[209] "Typora" "unbound" "vala" "VarScan"
[213] "vcftools" "VEGAS2" "verifyBamID" "VSCode"
[217] "VSCodium" "vte" "xpdf" "yaml-cpp"
[221] "Zotero" "zstd"
[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"
```

These are wrapped up as :star::star::star: **[modules](https://modules.readthedocs.io/en/latest/index.html)** :star::star::star:.
Expand Down Expand Up @@ -117,7 +117,7 @@ available from `/rds/project/jmmh2/software` but now `/rds/project/jmmh2/rds-jmm
largely be seen as sources which are used to build the reoository given above.

CEU users will be able to use `ANNOVAR`, `ensembl-vep`, `OpenMS`, `phenoscanner`, `polyphen`, `KentUtils`/`MAGMA`/`Pascal`/`VEGASV2`/`fgwas`/`locuszoom`
linking internal projects/personal space (additional requests need to be made). A large collection of R packages (1,415 as of 21/4/2024)
linking internal projects/personal space (additional requests need to be made). A large collection of R packages (1,419 as of 22/4/2024)
is linked with the latest R distribution, 4.3.3; there are also 10 packages under 4.3.3-gcc11 as well as 18 packages under 4.3.3-icelake. The small number of add-on packages have problems either at the compiling stage (because of higher version of gcc is required) or loading (i.e., compiled under 4.3.3 for cclake but cannot be used under icelake).

For CEU users, it is easy to point to them, e.g.,
Expand Down Expand Up @@ -317,6 +317,7 @@ Further information is avaiiable from **/usr/local/Cluster-Apps/ceuadmin/doc/ceu
| 2024-01-19 | htslib/1.19 | Genetics |
| 2024-01-24 | fraposa_pgsc/0.1.0 | Genetics[^fraposa] |
| "" | pgsc_calc/2.0.0-alpha.4 | Genetics[^pgsc_calc]|
| 2024-04-22 | peer/1.3 | Genetics[^peer] |

\* CEU or approved users only.

Expand Down Expand Up @@ -442,3 +443,22 @@ Further information is avaiiable from **/usr/local/Cluster-Apps/ceuadmin/doc/ceu

It appears quarto is called so presumably under icelake.


[^peer]: **peer**

An R package is associated with `ceuadmin/R`.

The following records its setup from conda, <https://www.biostars.org/p/9461665/>

```bash
module load miniconda/2
export mypath=/rds/project/jmmh2/rds-jmmh2-public_databases/software/peer/1.3
conda create --prefix=${mypath} -c conda-forge -c bioconda r-peer
conda activate /rds/project/jmmh2/rds-jmmh2-public_databases/peer/1.3
conda init bash
source ~/.bashrc
source activate ${mypath}
ln -s ${mypath} $CEUADMIN/peer/1.3
# This mirrors snakemake
# conda install -c conda-forge mamba
# mamba repoquery depends -a r-peer
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24 changes: 23 additions & 1 deletion systems/setup.md
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Expand Up @@ -267,6 +267,7 @@ All entries are ordered chronologically.
! "" | openssl/1.1.1b-icelake | Generic |
! "" | libssh2/1.11.0-icelake | Generic |
! "" | libssh/0.10.6-icelake | Generic |
! 2024-04-22 | peer/1.3 | Generic[^peer] |

\* CEU or approved users only.

Expand Down Expand Up @@ -896,4 +897,25 @@ Rscript -e '
make install
```

There remains an error message `git-remote-https: symbol lookup error: /usr/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b`.
There remains an error message `git-remote-https: symbol lookup error: /usr/lib64/libk5crypto.so.3: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b`.

[^peer]: **peer**

An R package is associated with `ceuadmin/R`.

The following records its setup from conda, <https://www.biostars.org/p/9461665/>

```bash
module load miniconda/2
export mypath=/rds/project/jmmh2/rds-jmmh2-public_databases/software/peer/1.3
conda create --prefix=${mypath} -c conda-forge -c bioconda r-peer
conda activate /rds/project/jmmh2/rds-jmmh2-public_databases/peer/1.3
conda init bash
source ~/.bashrc
source activate ${mypath}
ln -s ${mypath} $CEUADMIN/peer/1.3
# This mirrors snakemake
# conda install -c conda-forge mamba
# mamba repoquery depends -a r-peer
```

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