2-factor authentication (2FA)

This will become effective from 12 October 2023, for which MicroSoft authenticator app is required.

See also https://github.com/settings/security and https://docs.github.com/articles/about-two-factor-authentication for more information.

To save recovery code, visit https://github.com/settings/auth/recovery-codes.

For questions, visit https://support.github.com; for support, contact support via visiting The GitHub support page.

Git installation

Two instances are given below,

wget -qO- https://github.com/git/git/archive/v2.30.0.tar.gz | tar xfz -
cd git-2.30.0
make NO_GETTEXT=YesPlease install
# 2.38.1
wget -qO- https://github.com/git/git/archive/v2.38.1.tar.gz | tar xfz -
cd git-2.38.1
module load zlib/1.2.11
export ZLIB_PATH=/usr/local/Cluster-Apps/zlib/1.2.11/
# 2.44.0
wget -qO- https://github.com/git/git/archive/refs/tags/v2.44.0.tar.gz | x
tar xvfz -
cd git-2.44.0
make configure
configure --prefix=${CEUADMIN}/git/2.44.0-icelake
make
make install

and by default the executables will be put to ~/bin.

Git clone

Perhaps it is the most common use, e.g.,

git clone https://github.com/gkichaev/PAINTOR_V3.0.git
git clone https://github.com/gkichaev/PAINTOR_V3.0.wiki.git
git clone https://github.com/PMBio/peer PMBio

which download a repository, its wiki pages, and into a new directory, respectively. Use git pull to pull updates, which can be checked with git diff. When it shows following message

old mode 100644
new mode 100755

One can turn it off with git config core.filemode false.

It could be the appropriate way to download directory from a GitHub repository, e.g., git clone https://github.com/statgen/locuszoom.git for https://github.com/statgen/locuszoom/tree/develop/examples/data.

GitHub recovery

We resort to gitkraken (see below) to identify the date when the commit was made as with the associate hash from git log -- our example is based on repository jinghuazhao/R.

We now create a new branch, cherry-pick and commit to the branch.

git checkout -b recover
git cherry-pick a36d0974e9feec813e06620ccb9ba8ebc4e01ebf
git add .
git cherry-pick --continue
git push --set-upstream origin recover
git checkout master
git status

A pull request can be made from https://github.com/jinghuazhao/R/pull/new/recover

GitHub actions

Suppose our R packages are inside R folder, where we start some of the following script,

Rscript -e '
  library(usethis)
# https://github.com/r-lib/actions/tree/v2/examples
# https://www.tidyverse.org/blog/2022/06/actions-2-0-0/
  use_github_action("check-standard")
  use_github_action("test-coverage")
  use_github_action("pkgdown")
  use_github_action("bookdown")
  use_github_actions()
  use_github_actions_badge(name = "R-CMD-check.yaml", repo_spec = NULL)
  use_github_action_check_release(save_as = "R-CMD-check.yaml", ref = NULL, ignore = TRUE, open = FALSE)
# https://remotes.r-lib.org/articles/dependencies.html
'

The last line creates .github/workflows/R-CMD-check.yaml. We carry on adding a few other facilities from GitHub action, create workflow, create status badge, etc.

 <!-- badges: start -->
[![pages-build-deployment](https://github.com/jinghuazhao/R/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/jinghuazhao/R/actions/workflows/pages/pages-build-deployment)
[![CRAN Version](http://www.r-pkg.org/badges/version/gap)](https://cran.r-project.org/package=gap)
[![Monthly Downloads](http://cranlogs.r-pkg.org/badges/gap)](http://cranlogs.r-pkg.org/badges/gap)
[![Total Downloads](http://cranlogs.r-pkg.org/badges/grand-total/gap)](http://cranlogs.r-pkg.org/badges/grand-total/gap)
<!-- badges: end -->

which gives,

Note .github/workflows would contains actions which can be removed manually.

GitHub pages

This section involves npm which is described below.

Here we assume using of jekyll-rtd-theme, e.g., rundocs-jekyll-rtd-theme-v2.0.10-2-ge897694.zip.

module load python/3.7
source py37/bin/activate
pip install sphinx
pip install recommonmark
npm install --save-dev --save-exact prettier
npm install -g npm
npm install -g webpack
wget -qO- https://cache.ruby-lang.org/pub/ruby/3.0/ruby-3.0.2.tar.gz | tar xvfz -
cd ruby-3.0.2
./configure --prefix=${HPC_WORK}
make
make install
source ~/.bashrc
gem install jekyll bundler
bundle install
# unzip rundocs-jekyll-rtd-theme-v2.0.10-2-ge897694.zip
# mv rundocs-jekyll-rtd-theme-v2.0.10-2-ge897694 docs
# cd docs
# make build

Specific version can be attached, e.g., bundler:2.3.3. Relevant information can then be obtained, e.g.,

ruby -v
gem env
gem list

For update to 4.x, run gem update jekyll and specify gem "jekyll", "~> 4.0" in Gemfile. Some useful modules include kramdown-parser-gfm, github-pages.

When there is a conflict with Gemfile, we could use

mkdir docs
cd docs
/rds/user/${USER}/hpc-work/bin/jekyll new .
bundle update
# update Gemfile/_config.yml

One may prefix bundle exec to jekyll, e.g., bundle exec jekyll build.

... /ruby/3.1.0/bundler/runtime.rb:309:in check_for_activated_spec!': You have already activated i18n 1.9.1, but your Gemfile requires i18n 0.9.5. Prependingbundle exec` to your command may solve this.

It may also be simpler to remove system gem not used in a bundle bundle clean --force.

A specific plugin may also be installed, e.g.,

gem install jekyll-paginate

through which an appropriate version can be added to Gemfile followed by bundle commands above.

Consider YAML Validator and data files.

To generate a site map, follow these steps with jekyll/minima theme,

1. Add gem "jekyll-sitemap" to the plugin_groups of Gemfile.
2. Add - jekyll-sitemap to the plugins of _config.yml.
3. Modify assets/css/style.scss -- uncomment the default such that

@import
  "minima/skins/{{ site.minima.skin | default: 'classic' }}",
  "minima/initialize";

and cp -r ../../_sass/minima ., then we have the file sitemap.xml.

One may attempt to enable Google search, e.g., the post here.

The banner at cambridge-ceu.github.io is created as follows,

• Visit curtsy-alice-alice-in-wonderland-disney.gif.
• Select CAPTION at the bottom of the image, enter text with a customised color, and CREATE GIF.
• Crop the gif via https://onlinegiftools.com/crop-gif and embed it in the page.

Information regarding sass can be found here, https://sass-lang.com/.

ruby-install

By default, it is for root user and it is possible to do this locally,

mkdir -p $HOME/src
cd $HOME/src
wget -qO- ruby-install-0.8.3.tar.gz https://github.com/postmodern/ruby-install/archive/v0.8.3.tar.gz | \
tar -xzvf -
cd ruby-install-0.8.3/
PREFIX=${HPC_WORK} make install
ruby-install --latest --no-install-deps ruby

rvm

Web: https://rvm.io/.

Ruby Version Manager (RVM) is a command-line tool which allows you to easily install, manage, and work with multiple ruby environments from interpreters to sets of gems.

curl -sSL https://get.rvm.io | bash -s stable --rails

Note that for various ways of ruby installations, one may encounter problems with dtrace

linking miniruby
array.o: In function `empty_ary_alloc':
/home/jhz22/ruby-3.1.0/array.c:713: undefined reference to `ruby_array__create_semaphore'
array.o: In function `ary_new':
/home/jhz22/ruby-3.1.0/array.c:729: undefined reference to `ruby_array__create_semaphore'
/home/jhz22/ruby-3.1.0/array.c:729: undefined reference to `ruby_array__create_semaphore'
/home/jhz22/ruby-3.1.0/array.c:729: undefined reference to `ruby_array__create_semaphore'
array.o: In function `ec_ary_new':
/home/jhz22/ruby-3.1.0/array.c:817: undefined reference to `ruby_array__create_semaphore'
array.o:/home/jhz22/ruby-3.1.0/array.c:729: more undefined references to `ruby_array__create_semaphore' follow
eval.o: In function `setup_exception':
/home/jhz22/ruby-3.1.0/eval.c:618: undefined reference to `ruby_raise_semaphore'
eval.o:(.note.stapsdt+0x24): undefined reference to `ruby_raise_semaphore'
gc.o: In function `gc_prof_sweep_timer_start':
/home/jhz22/ruby-3.1.0/gc.c:12537: undefined reference to `ruby_gc__sweep__begin_semaphore'
gc.o: In function `gc_prof_sweep_timer_stop':
/home/jhz22/ruby-3.1.0/gc.c:12550: undefined reference to `ruby_gc__sweep__end_semaphore'
/home/jhz22/ruby-3.1.0/gc.c:12550: undefined reference to `ruby_gc__sweep__end_semaphore'
gc.o: In function `gc_prof_mark_timer_start':
/home/jhz22/ruby-3.1.0/gc.c:12514: undefined reference to `ruby_gc__mark__begin_semaphore'
gc.o: In function `gc_prof_mark_timer_stop':
/home/jhz22/ruby-3.1.0/gc.c:12525: undefined reference to `ruby_gc__mark__end_semaphore'
gc.o:(.note.stapsdt+0x24): undefined reference to `ruby_gc__sweep__end_semaphore'
gc.o:(.note.stapsdt+0x68): undefined reference to `ruby_gc__sweep__begin_semaphore'
gc.o:(.note.stapsdt+0xac): undefined reference to `ruby_gc__mark__end_semaphore'
gc.o:(.note.stapsdt+0xec): undefined reference to `ruby_gc__mark__begin_semaphore'
hash.o: In function `empty_hash_alloc':
/home/jhz22/ruby-3.1.0/hash.c:1542: undefined reference to `ruby_hash__create_semaphore'
hash.o:(.note.stapsdt+0x24): undefined reference to `ruby_hash__create_semaphore'
load.o: In function `rb_f_load':
/home/jhz22/ruby-3.1.0/load.c:784: undefined reference to `ruby_load__entry_semaphore'
/home/jhz22/ruby-3.1.0/load.c:794: undefined reference to `ruby_load__return_semaphore'
load.o: In function `require_internal':
/home/jhz22/ruby-3.1.0/load.c:1103: undefined reference to `ruby_require__entry_semaphore'
/home/jhz22/ruby-3.1.0/load.c:1113: undefined reference to `ruby_find__require__entry_semaphore'
/home/jhz22/ruby-3.1.0/load.c:1115: undefined reference to `ruby_find__require__return_semaphore'
/home/jhz22/ruby-3.1.0/load.c:1115: undefined reference to `ruby_find__require__return_semaphore'
/home/jhz22/ruby-3.1.0/load.c:1189: undefined reference to `ruby_require__return_semaphore'
/home/jhz22/ruby-3.1.0/load.c:1115: undefined reference to `ruby_find__require__return_semaphore'
load.o:(.note.stapsdt+0x24): undefined reference to `ruby_load__entry_semaphore'
load.o:(.note.stapsdt+0x7c): undefined reference to `ruby_load__return_semaphore'
load.o:(.note.stapsdt+0xd4): undefined reference to `ruby_require__entry_semaphore'
load.o:(.note.stapsdt+0x138): undefined reference to `ruby_find__require__entry_semaphore'
load.o:(.note.stapsdt+0x1a4): undefined reference to `ruby_find__require__return_semaphore'
load.o:(.note.stapsdt+0x210): undefined reference to `ruby_require__return_semaphore'
object.o: In function `class_call_alloc_func':
/home/jhz22/ruby-3.1.0/object.c:1958: undefined reference to `ruby_object__create_semaphore'
object.o:(.note.stapsdt+0x24): undefined reference to `ruby_object__create_semaphore'
parse.o: In function `yycompile0':
/home/jhz22/ruby-3.1.0/parse.y:6348: undefined reference to `ruby_parse__begin_semaphore'
/home/jhz22/ruby-3.1.0/parse.y:6350: undefined reference to `ruby_parse__end_semaphore'
parse.o:(.note.stapsdt+0x24): undefined reference to `ruby_parse__end_semaphore'
parse.o:(.note.stapsdt+0x7c): undefined reference to `ruby_parse__begin_semaphore'
string.o: In function `empty_str_alloc':
/home/jhz22/ruby-3.1.0/string.c:870: undefined reference to `ruby_string__create_semaphore'
string.o: In function `str_new0':
/home/jhz22/ruby-3.1.0/string.c:885: undefined reference to `ruby_string__create_semaphore'
/home/jhz22/ruby-3.1.0/string.c:885: undefined reference to `ruby_string__create_semaphore'
string.o: In function `str_new_static':
/home/jhz22/ruby-3.1.0/string.c:1003: undefined reference to `ruby_string__create_semaphore'
string.o: In function `rb_str_resurrect':
/home/jhz22/ruby-3.1.0/string.c:1816: undefined reference to `ruby_string__create_semaphore'
string.o:/home/jhz22/ruby-3.1.0/string.c:1823: more undefined references to `ruby_string__create_semaphore' follow
symbol.o: In function `dsymbol_alloc':
/home/jhz22/ruby-3.1.0/symbol.c:622: undefined reference to `ruby_symbol__create_semaphore'
symbol.o: In function `register_static_symid_str':
/home/jhz22/ruby-3.1.0/symbol.c:550: undefined reference to `ruby_symbol__create_semaphore'
symbol.o:(.note.stapsdt+0x24): undefined reference to `ruby_symbol__create_semaphore'
symbol.o:(.note.stapsdt+0x80): undefined reference to `ruby_symbol__create_semaphore'
vm.o: In function `vm_call_cfunc_with_frame':
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:3027: undefined reference to `ruby_cmethod__entry_semaphore'
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:3044: undefined reference to `ruby_cmethod__return_semaphore'
vm.o: In function `vm_dtrace':
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:4432: undefined reference to `ruby_method__entry_semaphore'
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:4432: undefined reference to `ruby_method__return_semaphore'
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:4433: undefined reference to `ruby_cmethod__entry_semaphore'
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:4434: undefined reference to `ruby_cmethod__return_semaphore'
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:4448: undefined reference to `ruby_cmethod__return_semaphore'
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:4445: undefined reference to `ruby_method__return_semaphore'
/home/jhz22/ruby-3.1.0/vm_insnhelper.c:4442: undefined reference to `ruby_cmethod__entry_semaphore'
vm.o: In function `rb_vm_pop_cfunc_frame':
/home/jhz22/ruby-3.1.0/vm.c:667: undefined reference to `ruby_cmethod__return_semaphore'
/home/jhz22/ruby-3.1.0/vm.c:667: undefined reference to `ruby_cmethod__return_semaphore'
vm.o: In function `hook_before_rewind':
/home/jhz22/ruby-3.1.0/vm.c:2051: undefined reference to `ruby_method__return_semaphore'
vm.o: In function `vm_exec_handle_exception':
/home/jhz22/ruby-3.1.0/vm.c:2257: undefined reference to `ruby_cmethod__return_semaphore'
vm.o: In function `vm_call0_cfunc_with_frame':
/home/jhz22/ruby-3.1.0/vm_eval.c:138: undefined reference to `ruby_cmethod__entry_semaphore'
/home/jhz22/ruby-3.1.0/vm_eval.c:155: undefined reference to `ruby_cmethod__return_semaphore'
vm.o: In function `vm_exec_core':
/home/jhz22/ruby-3.1.0/insns.def:462: undefined reference to `ruby_array__create_semaphore'
/home/jhz22/ruby-3.1.0/insns.def:473: undefined reference to `ruby_hash__create_semaphore'
/home/jhz22/ruby-3.1.0/insns.def:528: undefined reference to `ruby_hash__create_semaphore'
vm.o:(.note.stapsdt+0x24): undefined reference to `ruby_cmethod__entry_semaphore'
vm.o:(.note.stapsdt+0x94): undefined reference to `ruby_cmethod__return_semaphore'
vm.o:(.note.stapsdt+0x104): undefined reference to `ruby_cmethod__return_semaphore'
vm.o:(.note.stapsdt+0x174): undefined reference to `ruby_method__entry_semaphore'
vm.o:(.note.stapsdt+0x1e0): undefined reference to `ruby_method__return_semaphore'
vm.o:(.note.stapsdt+0x250): undefined reference to `ruby_cmethod__entry_semaphore'
vm.o:(.note.stapsdt+0x2c0): undefined reference to `ruby_cmethod__return_semaphore'
vm.o:(.note.stapsdt+0x330): undefined reference to `ruby_method__return_semaphore'
vm.o:(.note.stapsdt+0x3a0): undefined reference to `ruby_cmethod__return_semaphore'
vm.o:(.note.stapsdt+0x418): undefined reference to `ruby_cmethod__return_semaphore'
vm.o:(.note.stapsdt+0x48c): undefined reference to `ruby_cmethod__entry_semaphore'
vm.o:(.note.stapsdt+0x4fc): undefined reference to `ruby_array__create_semaphore'
vm.o:(.note.stapsdt+0x558): undefined reference to `ruby_hash__create_semaphore'
vm.o:(.note.stapsdt+0x5b0): undefined reference to `ruby_hash__create_semaphore'
yjit.o: In function `full_cfunc_return':
/home/jhz22/ruby-3.1.0/yjit_codegen.c:504: undefined reference to `ruby_cmethod__return_semaphore'
yjit.o:(.note.stapsdt+0x24): undefined reference to `ruby_cmethod__return_semaphore'
collect2: error: ld returned 1 exit status
make: *** [miniruby] Error 1

To get around one can use

configure --disable-dtrace --enable-shared --prefix=${HPC_WORK}
make
make install

Some details are described at here.

Finally, one can modify ext/Setup by uncommenting various options such as openssl, readline, zlib there, and also

configure --disable-dtrace --enable-shared --with-openssl --with-openssl-dir=${HPC_WORK}/openssl-1.1.1h --prefix=${HPC_WORK}
make
make install

GitHub landing pages

This is possible for two cases:

• User. Create a repository named as GitHub-username with a README.md.
• Organisation. Create a repository named as .github with a profile/README.md.
• Organisation members. Create a repository named as .github-private with a profile/README.md

For both user and organisation public access should be allowed, but organisation member would be private. To make sure image to be shown the syntax would be ![caption](absolute address), e.g., https://github.com/cambridge-ceu/.github/blob/master/profile/logo.png.

quarto

Web: https://quarto.org/

This provides a way to publish GitHub pages, see https://quarto.org/docs/publishing/github-pages.

On CSD3, one can invoke the quarto module,

# icelake
ssh login-q-1
module load ceuadmin/quarto

Technical information for the setup is described here, https://cambridge-ceu.github.io/csd3/applications/quarto.html.

GitHub themes

Two popular themes are as follows,

1. MkDocs, https://www.mkdocs.org/
2. Read the Docs, https://docs.readthedocs.io/en/stable/

Note that there is a specific MkDocs-mermaid2, https://pypi.org/project/mkdocs-mermaid2-plugin/#files, to be installed with python setup.py install.

npm

Web: https://nodejs.org/en/download/.

cd ${HPC_WORK}
wget -qO- https://nodejs.org/dist/v16.14.0/node-v16.14.0-linux-x64.tar.xz | \
tar xJf -
cd node-v16.14.0-linux-x64/
npm
npm install
npm install npm
npm install corepack

For intance, with make build for the jekyll-rtd-theme above we got error message,

node: relocation error: /usr/lib64/libnode.so.93: symbol FIPS_selftest, version OPENSSL_1_1_0g not defined in file libcrypto.so.1.1 with link time reference

we can issue npm rebuild to fix.

When the $HOME/node_modules/ was removed, we have an error message

npm ERR! could not determine executable to run

we do npm uninstall husky && npm install --save-dev husky@4 and also add --no-verify to git commit -m. As for missing package.json, we use npm init followed by npm install.

Note we have set prefix=${HOME}/.npm in ${HOME}/.npmrc.

When we receive message Error: could not determine executable to run, the following can be done.

rm -rf .git/hooks
npm install

Permissions

It may happen that you cannot enter your own directory: cd: v4: Permission denied, then it is fixed with

chmod u+rx,go-w v4

Equally, there might be problem to remove your own file, e.g., rm: cannot remove 'urls.txt': Permission denied, which can be resolved with resetting parent directory, i.e., chmod -R 777 v4.

In case there is confusion between cambridge-ceu repositories and your own, try these for the permission issues

ssh -vT git@github.com
ssh -T GitHub-username@github.com
git remote -v
git remote set-url origin https://github.com/cambridge-ceu/GitHub-matters.git
...
git push -f

For more details, see here.

Closely related are web pages such as SRCF, https://www.srcf.net/

chmod -R u+w,go-w,+rX /public/home/$USER/public_html

which applies four permissions changes:

• u+w (apply user-writable to all files)
• go-w (remove group/world-writable from all files)
• +r (make everything readable by everyone)
• +X (make directories executable i.e. openable)

Pop-up windows

A window may pop up for password, which could cause problems with command-line interface but this can be disabled with

 unset SSH_ASKPASS

or unset GIT_ASKPASS which could be part of .bashrc. Alternatively, this could be achieved with disabling DISPLAY, i.e.,

DISPLAY=
git push

Pull request

This is exemplified with TwoSampleMR. First create a branch with

git checkout -b jhz

As it uses roxygen, to export get_se add

#' @export

ahead of get_se in query.R and do the following,

devtools::install_dev_deps()
devtools::document()

and commit the changes. A related change to read_data.R regards

if ( log_pval )
{
       dat$pval <- 10^-dat$pval
}

which should have been

if ( log_pval )
{
       dat$pval <- 10^-dat[[pval]]
}

git add R/query.R
git commit -m "export get_se"
git add R/read_data.R
git commit -m "dat$pval <- 10^-dat[[pval]]"
git add NAMESPACE
git commit -m "export get_se"
git push --set-upstream origin jhz

making sure send a pull request from branch jhz.

Note also that to build TwoSampleMR on csd3, the following is necessary,

module load pandoc/2.0.6 pandoc-citeproc/0.12.2.2

One additional note concerns about automatic generation of documentation for R functions, through packages sinew and Roxygen2, respectively from CRAN.

REST API

Representational State Transfer (REST) (https://restfulapi.net/) allows for various operations on repositories, see https://docs.github.com/en/rest.

A shell application, curl, https://curl.se/ is used here.

curl https://api.github.com/zen

Keep it logically awesome.(base)

To simplify authentication and specifications we define environmental variables at the beginning, then create a reposity called blog, check its availability and delete it.

export user=<your-GitHub-username>
export token=<your-GitHub-token>
export API=https://api.github.com
export header="Accept: application/vnd.github.v3+json"
export name=blog

# 1. create the repository
curl -X POST -u $user:$token -H "$header" -d '{"name": "'"$name"'"}' $API/user/repos

# 2. list the repository
curl -H "$header" $API/repos/$user/$name

# 3. delete the repository
curl -X DELETE -u $user:$token -H "$header" $API/repos/$user/$name

Note that we also use the recommended header and mask the root URL (as API) to highlight the specifications /user/repos and repos/$user/blog.

Miscellaneous uses involving the cambridge-ceu site are as follows,

curl --version
curl https://api.github.com/ | jq
curl https://api.github.com/orgs/cambridge-ceu/repos
curl https://api.github.com/users/cambridge-ceu
curl https://api.github.com/users/cambridge-ceu/repos
curl https://api.github.com/users/cambridge-ceu/repos\?sort\=pushed

Where jq is the command-line JavaScript Object Notation (JSON) processor.

Some more useful examples are related to epigraphdb, eQTL Catalogue,

curl -X GET https://www.ebi.ac.uk/eqtl/api/studies | jq
curl -X GET https://www.ebi.ac.uk/eqtl/api/associations?variant_id=rs12075 > rs12075.json
curl -X GET https://www.ebi.ac.uk/eqtl/api/associations?variant_id=rs12075&study=Alasoo
curl -X 'POST' \
  'https://api.epigraphdb.org/protein/ppi' \
  -H 'accept: application/json' \
  -H 'Content-Type: application/json' \
  -d '{
  "uniprot_id_list": [
    "O14625", "P13500"
  ]
}' | jq
curl -X GET https://www.ebi.ac.uk/gwas/summary-statistics/api/traits?size=1000 | jq > gwas1000.json

and catalogueR,

options(width=150)
data.frame(epigraphdb::mr(outcome_trait = "Multiple sclerosis", pval_threshold = 1e-8))
library(catalogueR)
qtl.subset1 <- fetch_restAPI(unique_id=meta$unique_id[1], gwas_data=BST1)
qtl.subset2 <- fetch_tabix(unique_id=meta$unique_id[2], gwas_data=BST1)

where the last two statements wrap up the following lines,

http://www.ebi.ac.uk/eqtl/api/chromosomes/4/associations?paginate=False&study=Alasoo_2018&qtl_group=macrophage_naive&quant_method=ge&bp_lower=14737349&bp_upper=16737284
tabix ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/Alasoo_2018/ge/Alasoo_2018_ge_macrophage_naive.all.tsv.gz 4:14737349-16737284

respectively.

We carry on to postprocess the output above,

rs12075 <- jsonlite::fromJSON("rs12075.json")
link <- rs12075$`_links`$`next`$href
result <- do.call(rbind, lapply(rs12075$`_embedded`$associations, rbind))

and the results are as follows,

> link
[1] "http://www.ebi.ac.uk/eqtl/api/associations?size=20&start=20&links=False&variant_id=rs12075"
> result
      beta        maf      type  neg_log10_pvalue median_tpm pvalue   ref rsid      chromosome position  alt se        r2      ac
 [1,] 0.0103601   0.458333 "SNP" 0.1120341        0.6        0.77262  "G" "rs12075" "1"        159205564 "A" 0.0357159 0.99927 91
 [2,] 0.10655     0.458333 "SNP" 0.5001521        1.513      0.316117 "G" "rs12075" "1"        159205564 "A" 0.105527  0.99927 91
 [3,] 0.00471216  0.458333 "SNP" 0.02100965       5.229      0.952775 "G" "rs12075" "1"        159205564 "A" 0.0792819 0.99927 91
 [4,] 0.103534    0.458333 "SNP" 0.4388091        2.34       0.364075 "G" "rs12075" "1"        159205564 "A" 0.113328  0.99927 91
 [5,] 0.0322011   0.458333 "SNP" 0.1128161        0.827      0.77123  "G" "rs12075" "1"        159205564 "A" 0.110317  0.99927 91
 [6,] 0.0434981   0.458333 "SNP" 0.7434626        288.439    0.180525 "G" "rs12075" "1"        159205564 "A" 0.032158  0.99927 91
 [7,] -0.0241876  0.458333 "SNP" 0.5827094        195.988    0.261391 "G" "rs12075" "1"        159205564 "A" 0.0213623 0.99927 91
 [8,] -0.141131   0.458333 "SNP" 0.5962517        16.849     0.253366 "G" "rs12075" "1"        159205564 "A" 0.122543  0.99927 91
 [9,] 0.245207    0.458333 "SNP" 0.7806198        0.345      0.165722 "G" "rs12075" "1"        159205564 "A" 0.175061  0.99927 91
[10,] -0.0559002  0.458333 "SNP" 0.7160569        79.94      0.192284 "G" "rs12075" "1"        159205564 "A" 0.0424596 0.99927 91
[11,] -0.00890871 0.458333 "SNP" 0.0812611        991.08     0.829352 "G" "rs12075" "1"        159205564 "A" 0.0411791 0.99927 91
[12,] 0.0319441   0.458333 "SNP" 0.07365961       30.138     0.843996 "G" "rs12075" "1"        159205564 "A" 0.161729  0.99927 91
[13,] 0.0572641   0.458333 "SNP" 0.1638298        0.176      0.685757 "G" "rs12075" "1"        159205564 "A" 0.140938  0.99927 91
[14,] -0.00221514 0.458333 "SNP" 0.02556661       105.229    0.94283  "G" "rs12075" "1"        159205564 "A" 0.030778  0.99927 91
[15,] 0.148251    0.458333 "SNP" 0.85642          165.336    0.139181 "G" "rs12075" "1"        159205564 "A" 0.0991063 0.99927 91
[16,] -0.0631594  0.458333 "SNP" 0.1534025        0.089      0.702421 "G" "rs12075" "1"        159205564 "A" 0.16464   0.99927 91
[17,] 0.0820197   0.458333 "SNP" 0.4129235        0.048      0.386435 "G" "rs12075" "1"        159205564 "A" 0.0941081 0.99927 91
[18,] 0.130461    0.458333 "SNP" 0.7431741        0.559      0.180645 "G" "rs12075" "1"        159205564 "A" 0.0964765 0.99927 91
[19,] 0.0136613   0.458333 "SNP" 0.06425197       0.122      0.862478 "G" "rs12075" "1"        159205564 "A" 0.0785769 0.99927 91
[20,] -0.0935604  0.458333 "SNP" 0.6328566        0.6        0.232886 "G" "rs12075" "1"        159205564 "A" 0.0777485 0.99927 91
      variant              an  study_id      qtl_group         molecular_trait_id gene_id           tissue
 [1,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000143315"  "ENSG00000143315" "CL_0000235"
 [2,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000158477"  "ENSG00000158477" "CL_0000235"
 [3,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000158481"  "ENSG00000158481" "CL_0000235"
 [4,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000158485"  "ENSG00000158485" "CL_0000235"
 [5,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000158488"  "ENSG00000158488" "CL_0000235"
 [6,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000158710"  "ENSG00000158710" "CL_0000235"
 [7,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000158714"  "ENSG00000158714" "CL_0000235"
 [8,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000158716"  "ENSG00000158716" "CL_0000235"
 [9,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000162706"  "ENSG00000162706" "CL_0000235"
[10,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000162729"  "ENSG00000162729" "CL_0000235"
[11,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000162734"  "ENSG00000162734" "CL_0000235"
[12,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000163563"  "ENSG00000163563" "CL_0000235"
[13,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000163564"  "ENSG00000163564" "CL_0000235"
[14,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000163565"  "ENSG00000163565" "CL_0000235"
[15,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000163568"  "ENSG00000163568" "CL_0000235"
[16,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000177807"  "ENSG00000177807" "CL_0000235"
[17,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000181036"  "ENSG00000181036" "CL_0000235"
[18,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000213085"  "ENSG00000213085" "CL_0000235"
[19,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000256029"  "ENSG00000256029" "CL_0000235"
[20,] "chr1_159205564_G_A" 168 "Alasoo_2018" "macrophage_IFNg" "ENSG00000143315"  "ENSG00000143315" "CL_0000235"
>

Here are additional examples from GWAS Catalog, https://www.ebi.ac.uk/gwas/:

# GCST001729 requires API, https://www.ebi.ac.uk/gwas/summary-statistics/docs/
curl -X GET https://www.ebi.ac.uk/gwas/summary-statistics/api/associations?variant_id=rs601338
curl -X GET https://www.ebi.ac.uk/gwas/summary-statistics/api/studies/GCST001729/associations

In fact, in this case it might be handy to use gwasrapidd, https://cran.r-project.org/package=gwasrapidd, as follows,

rs601338 <- gwasrapidd::get_associations(variant_id = "rs601338")

Another useful REST API is LDlink.

Here this is another use for requesting data from the GREAT server as in the GitHub frea-pipeline repository,

curl -fsSG "http://bejerano.stanford.edu/great/public/cgi-bin/greatStart.php" \
     -d requestURL="http://web.mit.edu/aksarkar/great/$<" \
     -d bgURL="http://web.mit.edu/aksarkar/EnhClusters/$*.bed.gz" \
     -d requestSpecies=hg19 \
     -d outputType=batch -o $@

GWAS catalog summary statistics API, https://www.ebi.ac.uk/gwas/summary-statistics/docs/

GraphQL API

Hasura, https://cloud.hasura.io/

Open Targets Platform: https://platform.opentargets.org/api (Download datasets).

Updates on a forked repository

Once login, this turns to be very handy from the GitHub page by navigating to the code view (default), and pressing the following buttons,

• Contribute. To send a pull request to the upstream repository.
• Fetch upstream. To git pull from the upstream repository.

certification authority (CA)

An attempt to get away with the error message Peer's Certificate issuer is not recognized. is as follows,

mkdir ~/certs
curl https://curl.haxx.se/ca/cacert.pem -o ~/certs/cacert.pem
git config --global http.sslCAinfo "$HOME/certs/cacert.pem"

or from R

library(httr)
set_config(config(ssl_verifypeer = 0L))

gitkraken

cd ${HPC_WORK}
wget -qO- https://release.gitkraken.com/linux/gitkraken-amd64.tar.gz | \
tar xvfz -
cd bin
echo ${HPC_WORK}/gitkraken/gitkraken --no-sandbox $@ > gitkraken
chmod +x gitkraken

A CSD3 module has been made which can be loaded with module load ceuadmin/GitKraken.

ssh

The use of ssh involves several steps,

1. Generate private and public keys via ssh-keygen.
2. Paste the public key into your GitHub account profile.
3. Replace the url address at the .git/config locally with the repository address from its Code section (i.e., git@github.com:<username>/<repositoryname>.git).

This should enable code updates without request for the access token.

One see error

Warning: the ECDSA host key for 'github.com' differs from the key for the IP address '140.82.121.3'

then issue

ssh-keygen -R 140.82.121.3