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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
snakemake-5.24.1/docs/executing/cli.rst-104-
snakemake-5.24.1/docs/executing/cli.rst:105:Here, a folder ``myprofile`` is searched in per-user and global configuration directories (on Linux, this will be ``$HOME/.config/snakemake`` and ``/etc/xdg/snakemake``, you can find the answer for your system via ``snakemake --help``).
snakemake-5.24.1/docs/executing/cli.rst-106-Alternatively, an absolute or relative path to the folder can be given.
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snakemake-5.24.1/docs/executing/cloud.rst-32-
snakemake-5.24.1/docs/executing/cloud.rst:33:with ``$CLUSTER_NAME`` being the cluster name and ``$NODES`` being the number of cluster
snakemake-5.24.1/docs/executing/cloud.rst-34-nodes. If you intend to use google storage, make sure that ``--scopes storage-rw`` is set.
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snakemake-5.24.1/docs/executing/cloud.rst-81-In this mode, Snakemake will assume all input and output files to be stored in a given
snakemake-5.24.1/docs/executing/cloud.rst:82:remote location, configured by setting ``$REMOTE`` to your provider of choice
snakemake-5.24.1/docs/executing/cloud.rst:83:(e.g. ``GS`` for Google cloud storage or ``S3`` for Amazon S3) and ``$PREFIX``
snakemake-5.24.1/docs/executing/cloud.rst-84-to a bucket name or subfolder within that remote storage.
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snakemake-5.24.1/docs/executor_tutorial/azure_aks.rst-108-cluster <https://docs.microsoft.com/en-us/azure/aks/cluster-autoscaler>`__
snakemake-5.24.1/docs/executor_tutorial/azure_aks.rst:109:(``--enable-cluster-autoscaler``) called ``$clustername`` (i.e. ``snakemaks-aks``), which starts
snakemake-5.24.1/docs/executor_tutorial/azure_aks.rst-110-out with one node (``--node-count 1``) and has a maximum of three nodes
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snakemake-5.24.1/docs/project_info/faq.rst-265-A vim syntax highlighting definition for Snakemake is available `here <https://github.com/snakemake/snakemake/raw/master/misc/vim/syntax/snakemake.vim>`_.
snakemake-5.24.1/docs/project_info/faq.rst:266:You can copy that file to ``$HOME/.vim/syntax`` directory and add
snakemake-5.24.1/docs/project_info/faq.rst-267-
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snakemake-5.24.1/docs/project_info/faq.rst-272-
snakemake-5.24.1/docs/project_info/faq.rst:273:to your ``$HOME/.vimrc`` file. Highlighting can be forced in a vim session with ``:set syntax=snakemake``.
snakemake-5.24.1/docs/project_info/faq.rst-274-
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snakemake-5.24.1/docs/project_info/faq.rst-524- for f; do
snakemake-5.24.1/docs/project_info/faq.rst:525: touch -d @0`git log --pretty=%at -n1 -- "$f"` "$f"
snakemake-5.24.1/docs/project_info/faq.rst-526- done
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snakemake-5.24.1/docs/snakefiles/deployment.rst-111-
snakemake-5.24.1/docs/snakefiles/deployment.rst:112:Snakemake will store the environment persistently in ``.snakemake/conda/$hash`` with ``$hash`` being the MD5 hash of the environment definition file content. This way, updates to the environment definition are automatically detected.
snakemake-5.24.1/docs/snakefiles/deployment.rst-113-Note that you need to clean up environments manually for now. However, in many cases they are lightweight and consist of symlinks to your central conda installation.
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snakemake-5.24.1/docs/snakefiles/modularization.rst-73-It is advisable to use a github URL that includes the commit as above instead of a branch name, in order to ensure reproducible results.
snakemake-5.24.1/docs/snakefiles/modularization.rst:74:Snakemake will execute the rule by invoking `cwltool`, which has to be available via your `$PATH` variable, and can be, e.g., installed via `conda` or `pip`.
snakemake-5.24.1/docs/snakefiles/modularization.rst-75-When using in combination with :ref:`--use-singularity <singularity>`, Snakemake will instruct `cwltool` to execute the command via Singularity in user space.
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snakemake-5.24.1/docs/snakefiles/rules.rst-656- ## Source
snakemake-5.24.1/docs/snakefiles/rules.rst:657: <a download="report.Rmd" href="`r base64enc::dataURI(file = params$rmd, mime = 'text/rmd', encoding = 'base64')`">R Markdown source file (to produce this document)</a>
snakemake-5.24.1/docs/snakefiles/rules.rst-658-
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snakemake-5.24.1/misc/vim/README.md-1-A vim syntax highlighting definition for Snakemake.
snakemake-5.24.1/misc/vim/README.md:2:You can copy the `snakemake.vim` file to `$HOME/.vim/syntax` directory and add
snakemake-5.24.1/misc/vim/README.md-3-
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snakemake-5.24.1/misc/vim/README.md-8-
snakemake-5.24.1/misc/vim/README.md:9:to your `$HOME/.vimrc` file. Highlighting can be forced in a vim session with `:set syntax=snakemake`.
snakemake-5.24.1/misc/vim/README.md-10-
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snakemake-5.24.1/snakemake/executors/__init__.py-2100- # benchmarking at all. We benchmark this process unless the
snakemake-5.24.1/snakemake/executors/__init__.py:2101: # execution is done through the ``shell:``, ``script:``, or
snakemake-5.24.1/snakemake/executors/__init__.py-2102- # ``wrapper:`` stanza.
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snakemake-5.24.1/snakemake/report/report.html-622- function show_rule_properties(rule) {
snakemake-5.24.1/snakemake/report/report.html:623: $(`.rule-properties[data-rule=${rule}]`).modal("show");
snakemake-5.24.1/snakemake/report/report.html-624- }
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snakemake-5.24.1/snakemake/report/report.html-640- {% if mode_embedded %}