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jinghuazhao committed Apr 23, 2024
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164 changes: 15 additions & 149 deletions systems/ceuadmin.md
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Expand Up @@ -240,17 +240,17 @@ Further information is avaiiable from **/usr/local/Cluster-Apps/ceuadmin/doc/ceu
| "" | samtools/1.11 | Genetics |
| "" | bcftools/1.12 | Genetics |
| "" | MORGAN/3.4 | Genetics |
| "" | METAL/2020-05-05r | Genetics[^metal] |
| "" | METAL/2020-05-05r | Genetics |
| "" | regenie/3.2.1 | Genetics |
| "" | GEMMA/0.98.5 | Genetics[^gemma] |
| "" | GEMMA/0.98.5 | Genetics |
| "" | htslib/1.12 | Genetics |
| "" | fcGENE/1.0.7 | Genetics[^fcgene] |
| "" | fcGENE/1.0.7 | Genetics |
| "" | 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 | Genetics[^qtltools] |
| "" | QTLtools/1.3.1-25 | Genetics |
| "" | blat/37x1 | Genetics |
| "" | bedtools2/2.29.2 | Genetics |
| "" | bedops/2.4.41 | Genetics |
Expand All @@ -265,22 +265,22 @@ Further information is avaiiable from **/usr/local/Cluster-Apps/ceuadmin/doc/ceu
| "" | CAVIAR/2.2 | Genetics |
| "" | MONSTER/1.3 | Genetics |
| "" | osca/0.46 | Genetics |
| "" | LEMMA/1.0.4 | Genetics[^lemma] |
| "" | LEMMA/1.0.4 | Genetics |
| "" | 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\*[^openms] |
| "" | OpenMS/3.0.0 | Genetics\* |
| "" | 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\*[^lz] |
| 2022-11-21 | locuszoom/1.4 | Genetics\* |
| "" | DEPICT/v1_rel194 | Genetics\* |
| "" | MAGMA/1.10 | Genetics\* |
| "" | Pascal/v_debut | Genetics\* |
Expand All @@ -293,10 +293,10 @@ Further information is avaiiable from **/usr/local/Cluster-Apps/ceuadmin/doc/ceu
| 2023-02-01 | GENEHUNTER/2.1_r6 | Genetics |
| 2023-03-14 | regenie/3.2.5 | Genetics |
| 2023-03-24 | PoGo/1.0.0 | Genetics |
| 2023-03-31 | PWCoCo/2023-03-31 | Genetics[^pwcoco] |
| 2023-03-31 | PWCoCo/2023-03-31 | Genetics |
| 2023-04-02 | regenie/3.2.5.3 | Genetics |
| 2023-04-04 | PWCoCo/1.0 | Genetics |
| 2023-06-02 | regenie/3.2.7 | Genetics[^regenie] |
| 2023-06-02 | regenie/3.2.7 | Genetics |
| 2023-06-06 | allegro/2.0f | Genetics |
| 2023-06-19 | plink-ng/2.00a3.3 | Genetics |
| 2023-06-26 | RHHsoftware/0.1 | Genetics |
Expand All @@ -307,17 +307,17 @@ Further information is avaiiable from **/usr/local/Cluster-Apps/ceuadmin/doc/ceu
| "" | sra-tools/3.0.8 | Genetics |
| "" | gatk/4.4.0.0 | Genetics |
| 2023-11-24 | ldsc/1.0.1 | Genetics |
| 2023-11-30 | gdc/1.6.1-1.0.0 | Genetics[^gdc] |
| 2023-11-30 | gdc/1.6.1-1.0.0 | Genetics |
| 2023-12-20 | verifyBamID/1.1.3 | Genetics |
| 2023-12-21 | verifyBamID/2.0.1 | Genetics |
| 2023-12-27 | regtools/1.0.0 | Genetics[^regtools] |
| "" | VarScan/2.4.6 | Genetics[^varscan] |
| 2023-12-27 | regtools/1.0.0 | Genetics |
| "" | VarScan/2.4.6 | Genetics |
| 2024-01-08 | picard/3.1.1 | Genetics |
| "" | plink/2.0_20240105 | Genetics |
| 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] |
| 2024-01-24 | fraposa_pgsc/0.1.0 | Genetics |
| "" | pgsc_calc/2.0.0-alpha.4 | Genetics |
| 2024-04-22 | peer/1.3 | Genetics |

\* CEU or approved users only.

Expand All @@ -328,137 +328,3 @@ Further information is avaiiable from **/usr/local/Cluster-Apps/ceuadmin/doc/ceu
[^gui]: **GUI**

As GUI-based programs claim more computing resources, it is recommended that they are only used occasionally, e.g., calling back GitHub sessions.

[^metal]: **metal**

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 in `2020-05-05r` indicates a replacement of functions in `libsrc/MathStats.cpp` to ensure generality -- [details](files/complaint.pdf) have also been posted to the GitHub page, [https://github.com/statgen/METAL/issues/24](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.
```

[^gemma]: **gemma**

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.

```bash
module load openblas/0.2.15
make
```

[^fcgene]: **fcgene**

Alternative site

See [https://github.com/dr-roshyara/fcgene](https://github.com/dr-roshyara/fcgene)

[^qtltools]: **qtltools**

The long version number is 1.3.1-25-g6e49f85f20.

[^lemma]: **lemma**

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.

[^openms]: **openms**

When the OpenMS module is loaded, pyopenms and alphapept also become available.

[^lz]: **locuszoom**

The version adds chromosome X data and will have options using INTERVAL data.

[^pwcoco]: **pwcoco**

It compiles under gcc/9. Upon release of 1.1, this snapshot is removed.

[^regenie]: **regenie**

Building regenie 3.2.7

```bash
cd ~/rds/public_databases/software/
wget -qO- https://github.com/rgcgithub/regenie/archive/refs/tags/v3.2.7.tar.gz | \
tar xvfz -
cd regenie-3.2.7/
export BGEN_PATH=~/rds/public_databases/software/bgen
module load zlib/1.2.11
export ZLIB_LIBRARY=/usr/local/Cluster-Apps/zlib/1.2.11
module load gcc/6
module load cmake-3.19.7-gcc-5.4-5gbsejo
module load intel/mkl/mic/2018.4
mkdir build
cd build
cmake ..
make
```

[^gdc]: **gdc**

It also includes gdc_dtt-ui 1.0.0

[^regtools]: **regtools**

gcc/6 is required for C++11.

[^varscan]: **varscan**

Simply call `java -jar $VARSCAN_HOME/VarScan.v2.4.6.jar` after `module load ceuadmin/VarScan/2.4.6`.

[^fraposa]: **fraposa**

Several packages, including poetry, poetry-plugin-export and fraposa_pgsc, will be installed as follows,

```bash
module load ceuadmin/Anaconda3/2023.09-0
pip install poetry
pip3 install poetry-plugin-export
pip install --use-feature=fast-deps .
scripts/run_example.sh
```

This is necessay since by default `peotry install` will use user's home directory. As indicated from `poetry install --help`:

The install command reads the poetry.lock file from
the current directory, processes it, and downloads and installs all the
libraries and dependencies outlined in that file. If the file does not
exist it will look for pyproject.toml and do the same.

[^pgsc_calc]: **pgsc_calc**

Application, <https://pgsc-calc.readthedocs.io/en/latest/index.html>

```bash
nextflow run pgscatalog/pgsc_calc -profile test,singularity
```

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
source activate ${mypath}
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
21 changes: 20 additions & 1 deletion systems/setup.md
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Expand Up @@ -901,7 +901,25 @@ Rscript -e '

[^peer]: **peer**

An R package is associated with `ceuadmin/R`.
An R package is done as follows,

```bash
git clone https://github.com/PMBio/peer PMBio
cd PMBio
module load cmake/2.8 python/2.7
mkdir build && cd build
module load R/3.4
cmake -DBUILD_R_PACKAGE=1 ..
make
## build/ version
cd R
R CMD INSTALL peer -l ..
## cran/ version
cd ../../cran
R CMD INSTALL peer -l ..
```

Therefore the R package has to be called using module `R/3.4`, such as `library(peer,lib.loc='/rds/project/jmmh2/rds-jmmh2-public_databases/software/peer/PMBio')`.

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

Expand All @@ -919,3 +937,4 @@ Rscript -e '
# mamba repoquery depends -a r-peer
```

Overall, these appear to be outdated if other R packages are called unless they are also installed.

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