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Update build instructions for v0.2.0-m10
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petebankhead committed Apr 22, 2020
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10 changes: 9 additions & 1 deletion docs/intro/citing.md
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Expand Up @@ -26,7 +26,7 @@ The following key indicates what, if anything, was cited in the main references
### Contents

* [2020](#2020) (55)
* [2020](#2020) (59)
* [2019](#2019) (144)
* [2018](#2018) (48)
* [2017](#2017) (5)
Expand Down Expand Up @@ -80,6 +80,8 @@ Myeloid and T Cell Responses. **Cell Reports**. https://doi.org/10.1016/j.celrep

1. Goto, Y. et al. (2020). Muscarinic receptors promote castration-resistant growth of prostate cancer through a FAK–YAP signaling axis. **Oncogene**. https://doi.org/10.1038/s41388-020-1272-x 📗

1. Gualandi, M. et al. (2020). Oncogenic ALK<sup>F1174L</sup> drives tumorigenesis in cutaneous squamous cell carcinoma. **Life Science Alliance**. https://dx.doi.org/10.26508/lsa.201900601 📗

1. Gupta, S. et al. (2020). Digital quantitative assessment of PD-L1 using digital spatial profiling. **Laboratory Investigation**. https://doi.org/10.1038/s41374-020-0424-5 📗

1. Herrspiegel, C. et al. (2020). Digital morphometry of tumor nuclei correlates to BAP-1 status, monosomy 3, gene expression class and survival in uveal melanoma. **Experimental Eye Research**. https://doi.org/10.1016/j.exer.2020.107987 📗
Expand All @@ -92,6 +94,8 @@ Myeloid and T Cell Responses. **Cell Reports**. https://doi.org/10.1016/j.celrep

1. Kelly, L. et al. (2020). Increased Hypothalamic Projections to the Lateral Hypothalamus and Responses to Leptin in Rat Neonates From High Fat Fed Mothers. **Frontiers in Neuroscience**. https://doi.org/10.3389/fnins.2019.01454 📗

1. Kim, J. H. et al. (2020). Multi-Spheroid-Loaded Human Acellular Dermal Matrix Carrier Preserves Its Spheroid Shape and Improves In Vivo Adipose-Derived Stem Cell Delivery and Engraftment. **Tissue Engineering and Regenerative Medicine**. https://doi.org/10.1007/s13770-020-00252-w 📗

1. Kim, Y. et al. (2020). Identification and Validation of VEGFR2 Kinase as a Target of Voacangine by a Systematic Combination of DARTS and MSI. **Biomolecules**. https://doi.org/10.3390/biom10040508 📗

1. Kim, Y. et al. (2020). Protein Expression in Metastatic Melanoma and the Link to Disease Presentation in a Range of Tumor Phenotypes. **Cancers**. https://doi.org/10.3390/cancers12030767 📗
Expand All @@ -106,6 +110,8 @@ Myeloid and T Cell Responses. **Cell Reports**. https://doi.org/10.1016/j.celrep

1. Liu, J. Y. W. et al. (2020). Granule Cell Dispersion in Human Temporal Lobe Epilepsy: Proteomics Investigation of Neurodevelopmental Migratory Pathways. **Frontiers in Cellular Neuroscience**. https://doi.org/10.3389/fncel.2020.00053 📗

1. Liu, Y. et al. (2020). TSP1‐CD47‐SIRPα signaling facilitates the development of endometriosis by mediating the survival of ectopic endometrium. **American Journal of Reproductive Immunology**. https://doi.org/10.1111/aji.13236 📗

1. Mannix, R. et al. (2020). Internal jugular vein compression collar mitigates histopathological alterations after closed head rotational head impact in swine: A pilot study. **Neuroscience**. https://doi.org/10.1016/j.neuroscience.2020.04.009 😞

1. Marotte, L. et al. (2020). Increased antitumor efficacy of PD-1-deficient melanoma-specific human lymphocytes. **Journal for ImmunoTherapy of Cancer**. http://dx.doi.org/10.1136/jitc-2019-000311 📗
Expand Down Expand Up @@ -142,6 +148,8 @@ Myeloid and T Cell Responses. **Cell Reports**. https://doi.org/10.1016/j.celrep

1. Tedeschi, A. et al. (2020). Cep55 promotes cytokinesis of neural progenitors but is dispensable for most mammalian cell divisions. **Nature Communications**. https://doi.org/10.1038/s41467-020-15359-w 📗

1. Tiwari, L. et al. (2020). Clinico‐pathological correlation of optical fluorescence imaging in oral mucosal lesions. **Oral Diseases**. https://doi.org/10.1111/odi.13334 📗

1. Xie, C. et al. (2020). Immune checkpoint blockade in combination with stereotactic body radiotherapy in patients with metastatic pancreatic ductal adenocarcinoma. **Clinical Cancer Research**. https://doi.org/10.1158/1078-0432.CCR-19-3624 😞

[Top](#contents)
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101 changes: 11 additions & 90 deletions docs/reference/building.rst
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Expand Up @@ -26,7 +26,7 @@ Step 1: Installing prerequisites
Install a Java Development Kit (JDK)
====================================

QuPath requires OpenJDK 11 (or later).
QuPath requires OpenJDK 14 (or later).
Typically, the latest stable JDK is used.
There are a few places where you can find pre-built OpenJDK binaries - a popular source is AdoptOpenJDK_.

Expand All @@ -41,22 +41,6 @@ There are a few places where you can find pre-built OpenJDK binaries - a popular
If you can't (e.g. because of some other Java software needing the PATH set to something else) I'm afraid I'll leave resolving that up to you.


Download the latest JPackage
============================

.. sidebar:: JDK 14

If you're using JDK 14 (to be released March 2020) then you should already have *jpackage* - no need to install it separately.

To create the QuPath installer, you'll need *jpackage*.

For now, you need to download an early access build separately from jdk.java.net_.

.. _jdk.java.net: https://jdk.java.net/jpackage

Extract the contents (e.g. right-click and unzip) to a folder of your choosing *and remember where it is because you'll need the path to that folder later*.


==================================
Step 2: Get the QuPath source code
==================================
Expand Down Expand Up @@ -87,69 +71,8 @@ If you're using either Mac or Windows, the following steps may help.
Therefore you'll need another desktop client, or handle Git from the command line.


====================================
Step 3: Add a gradle.properties file
====================================

Go to GitHub Desktop, make sure that the :guilabel:`Current repository` is :guilabel:`qupath` and choose :menuselection:`Repository --> Open in Atom`

.. figure:: images/building-github-desktop-project.png
:class: shadow-image
:align: center
:width: 50%


Under the :guilabel:`Project` tab on the left within *Atom*, right-click on the top 'qupath' and choose :menuselection:`New File`.

.. figure:: images/building-properties-create.png
:class: shadow-image
:align: center
:width: 50%

When prompted to *Enter the path for the new file* type ``gradle.propertes``

.. figure:: images/building-properties.png
:class: shadow-image
:align: center
:width: 75%


Inside *gradle.properties*, enter the following text

.. code-block:: bash
packager=/path/to/jpackage
where you'll need to replace ``/path/to/jpackage`` with the actual path.

.. note::

If you're using JDK 14 or later for everything, you probably don't need to set *jpackage* inside *gradle.properties* at all.

Otherwise, it should be found somewhere inside the folder you extracted earlier.
On Windows, the path you need should look something like this:

.. code-block:: bash
packager=C:/Users/myname/Documents/jpackage/jdk-14/bin/jpackage.exe
.. tip::

If you *want*, you can add extra information to *gradle.properties* to customize how QuPath is built (or how quickly it is built), e.g.

.. code-block:: bash
// Essential if using a JDK < JDK 14!
packager=/path/to/jpackage
// Optional
org.gradle.parallel=true // If you are impatient
org.gradle.java.home=/path/to/another/jdk // If you want to use a different JDK to build QuPath from the system default
request-git-tag=true // If you installed Git & want to know *exactly* what was the last commit prior to building the software
================================
Step 4: Build QuPath with Gradle
Step 3: Build QuPath with Gradle
================================

Open the QuPath source directory in a command prompt
Expand All @@ -172,13 +95,13 @@ At the command prompt, type the following:

.. code-block:: bash
gradlew createPackage
gradlew clean build createPackage
for Windows, or

.. code-block:: bash
./gradlew createPackage
./gradlew clean build createPackage
for MacOS and Linux.

Expand Down Expand Up @@ -223,15 +146,7 @@ When this happens, it's worth running
gradlew clean
to clean up old files that could be causing trouble.
You can also combine the options, e.g.
.. code-block:: bash
gradlew clean createPackage -Ptype=installer
will clean first, build QuPath & create an installer all in one go.
once or twice extra to clean up old files that could be causing trouble.


Getting the latest updates
Expand Down Expand Up @@ -309,3 +224,9 @@ To generate javadocs for the source code, use
gradlew mergedJavadocs
This will generate html javadocs in a ``./build/merged-docs`` subdirectory.

If you'd like to include external links to other relevant javadocs (e.g. for the JDK, ImageJ, JTS) use

.. code-block:: bash
gradlew mergedJavadocs -PlinkJavadoc=true

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