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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/toil/commit/2532f726bf8795142aa282837dca98c0a0c6973d">2532f726</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-07-29T18:26:27Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Delete spelling</pre>
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<h4>1 changed file:</h4>
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<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
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−
debian/patches/spelling
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<h4>Changes:</h4>
<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<a href="https://salsa.debian.org/med-team/toil/commit/2532f726bf8795142aa282837dca98c0a0c6973d#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Subject: Lintian-inspired spelling fixes</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/docs/running/cloud/amazon.rst</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/docs/running/cloud/amazon.rst</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -165,7 +165,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> When using the Toil provisioner, the appliance image will be automatically chosen</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> based on the pip-installed version of Toil on your system. That choice can be</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- overriden by setting the environment variables ``TOIL_DOCKER_REGISTRY`` and ``TOIL_DOCKER_NAME`` or</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ overridden by setting the environment variables ``TOIL_DOCKER_REGISTRY`` and ``TOIL_DOCKER_NAME`` or</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> ``TOIL_APPLIANCE_SELF``. See :ref:`envars` for more information on these variables. If</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> you are developing with autoscaling and want to test and build your own</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> appliance have a look at :ref:`appliance_dev`.</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/docs/running/cloud/gce.rst</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/docs/running/cloud/gce.rst</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -32,7 +32,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> $ chmod 400 ~/.ssh/id_rsa ~/.ssh/id_rsa.pub</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#. Add your newly formated public key to Google. To do this, log into your Google Cloud account</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#. Add your newly formatted public key to Google. To do this, log into your Google Cloud account</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> and go to `metadata`_ section under the Compute tab.</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> .. image:: googleScreenShot.png</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/docs/running/cwl.rst</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/docs/running/cwl.rst</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> ------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> A CWL workflow can be run indirectly in a native Toil script. However, this is not the :ref:`standard <cwl>` way to run</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CWL workflows with Toil and doing so comes at the cost of job efficency. For some use cases, such as running one process on</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CWL workflows with Toil and doing so comes at the cost of job efficiency. For some use cases, such as running one process on</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> multiple files, it may be useful. For example, if you want to run a CWL workflow with 3 YML files specifying different</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> samples inputs, it could look something like::</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/docs/running/wdl.rst</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/docs/running/wdl.rst</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="p">@@ -117,7 +117,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> A cromwell.jar file is needed in order to run a WDL workflow.</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> A WDL workflow can be run indirectly in a native Toil script. However, this is not the :ref:`standard <wdl>` way to run</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-WDL workflows with Toil and doing so comes at the cost of job efficency. For some use cases, such as running one process on</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+WDL workflows with Toil and doing so comes at the cost of job efficiency. For some use cases, such as running one process on</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> multiple files, it may be useful. For example, if you want to run a WDL workflow with 3 JSON files specifying different</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"> samples inputs, it could look something like::</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/jobStores/abstractJobStore.py</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/jobStores/abstractJobStore.py</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="p">@@ -758,7 +758,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> def jobs(self):</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> Best effort attempt to return iterator on all jobs in the store. The iterator may not</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return all jobs and may also contain orphaned jobs that have already finished succesfully</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return all jobs and may also contain orphaned jobs that have already finished successfully</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> and should not be rerun. To guarantee you get any and all jobs that can be run instead</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> construct a more expensive ToilState object</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/lib/threading.py</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/lib/threading.py</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="p">@@ -39,7 +39,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> class ExceptionalThread(threading.Thread):</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> A thread whose join() method re-raises exceptions raised during run(). While join() is</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- idempotent, the exception is only during the first invocation of join() that succesfully</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ idempotent, the exception is only during the first invocation of join() that successfully</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> joined the thread. If join() times out, no exception will be re reraised even though an</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> exception might already have occured in run().</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/src/toil/job.py</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/src/toil/job.py</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="p">@@ -273,11 +273,11 @@</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> exhausting all their retries, remove any successor jobs and rerun this job to restart the</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> subtree. Job must be a leaf vertex in the job graph when initially defined, see</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> :func:`toil.job.Job.checkNewCheckpointsAreCutVertices`.</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- :type cores: int or string convertable by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- :type disk: int or string convertable by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ :type cores: int or string convertible by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ :type disk: int or string convertible by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> :type preemptable: bool</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- :type cache: int or string convertable by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- :type memory: int or string convertable by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ :type cache: int or string convertible by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ :type memory: int or string convertible by toil.lib.humanize.human2bytes to an int</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> requirements = {'memory': memory, 'cores': cores, 'disk': disk,</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> 'preemptable': preemptable}</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/docs/appendices/environment_vars.rst</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/docs/appendices/environment_vars.rst</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="p">@@ -28,7 +28,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> | TOIL_DOCKER_REGISTRY | The URL of the registry of the Toil Appliance |</span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"> | | image you wish to use. Docker will use Dockerhub |</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"> | | by default, but the quay.io registry is also |</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-| | very popular and easily specifiable by settting |</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+| | very popular and easily specifiable by setting |</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"> | | this option to ``quay.io``. |</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"> +------------------------+----------------------------------------------------+</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"> | TOIL_DOCKER_NAME | The name of the Toil Appliance image you |</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- toil.orig/docs/developingWorkflows/developing.rst</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ toil/docs/developingWorkflows/developing.rst</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="p">@@ -559,7 +559,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"> Just like regular promises, the return value must be determined prior to</span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"> scheduling any job that depends on the return value. In our example above, notice</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- how the dependant jobs were follow ons to the parent while promising jobs are</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ how the dependent jobs were follow ons to the parent while promising jobs are</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"> children of the parent. This ordering ensures that all promises are</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"> properly fulfilled.</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"> </span></pre>
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