add new 30 projects (#57)

Co-authored-by: Philip Colmer <1979931+pcolmer@users.noreply.github.com>
Co-authored-by: Zhenyu Zheng <zheng.zhenyu@outlook.com>

_posts/2021-08-31-BamTools.md

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+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "BamTools"
+
+project:
+  title: "BamTools"
+  type: "C++"
+  url: "https://github.com/pezmaster31/bamtools"
+  project_official_url: "https://github.com/pezmaster31/bamtools"
+  logo: "/assets/images/projects/hpc/bamtools/logo.png"
+  overview: "BamTools provides both a programmer's API and an end-user's toolkit for handling
+BAM files."
+
+supported_releases:
+  - release:
+    version: "v2.5.2"
+    url: "https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.2.tar.gz"
+  - release:
+    version: "v2.5.1"
+    url: "https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.1.tar.gz"
+  - release:
+    version: "v2.5.0"
+    url: "https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.0.tar.gz"
+---
+
+<p>BamTools</p>

_posts/2021-08-31-BerkeleyGW.md

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+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "BerkeleyGW"
+
+project:
+  title: "BerkeleyGW"
+  type: "C++"
+  url: "https://berkeleygw.org/"
+  project_official_url: "https://gitlab.com/mbarbry/berkeley-gw"
+  logo: "/assets/images/projects/hpc/berkeleygw/logo.png"
+  overview: "BerkeleyGW is a many-body perturbation theory code for excited states, using the GW method and the GW plus Bethe-Salpeter equation (GW-BSE) method to solve respectively for quasiparticle excitations and optical properties of materials."
+
+supported_releases:
+  - release:
+    version: "3.0.1"
+    url: "https://app.box.com/s/m1dgnhiemo47lhxczrn6si71bwxoxor8"
+  - release:
+    version: "3.0"
+    url: "https://app.box.com/s/lp6hj4kxr459l5a6t05qfuzl2ucyo03q"
+---
+
+<p>BerkeleyGW</p>

_posts/2021-08-31-Falcon.md

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+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "Falcon"
+
+project:
+  title: "Falcon"
+  type: "Python"
+  url: "https://falcon.readthedocs.io/en/stable/"
+  project_official_url: "https://github.com/falconry/falcon"
+  logo: "/assets/images/projects/hpc/falcon/logo.jpg"
+  overview: "Falcon is a minimalist ASGI/WSGI framework for building mission-critical REST APIs and microservices, with a focus on reliability, correctness, and performance at scale."
+
+supported_releases:
+  - release:
+    version: "3.1.1"
+    url: "https://github.com/falconry/falcon/releases/download/3.1.1/falcon-3.1.1-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
+  - release:
+    version: "3.1.0"
+    url: "https://github.com/falconry/falcon/releases/download/3.1.0/falcon-3.1.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
+  - release:
+    version: "3.0.1"
+    url: "https://github.com/falconry/falcon/releases/download/3.0.1/falcon-3.0.1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
+---
+
+<p>Falcon</p>

_posts/2021-08-31-FigTree.md

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+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "FigTree"
+
+project:
+  title: "FigTree"
+  type: "Java"
+  url: "https://github.com/rambaut/figtree"
+  project_official_url: "https://github.com/rambaut/figtree"
+  logo: "/assets/images/projects/hpc/figtree/logo.png"
+  overview: "FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST."
+
+supported_releases:
+  - release:
+    version: "v1.4.4"
+    url: "https://github.com/rambaut/figtree/archive/refs/tags/v1.4.4.tar.gz"
+  - release:
+    version: "v1.4.3"
+    url: "https://github.com/rambaut/figtree/archive/refs/tags/v1.4.3.tar.gz"
+---
+
+<p>FigTree</p>

_posts/2021-08-31-Fio.md

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+---
+layout: project
+permalink: /:title/
+category: libraries
+
+meta:
+  keywords: "Fio"
+
+project:
+  title: "Fio"
+  type: "C"
+  url: "https://fio.readthedocs.io/en/latest/fio_doc.html"
+  project_official_url: "https://github.com/axboe/fio"
+  logo: "/assets/images/projects/libraries/fio/logo.png"
+  overview: "Fio spawns a number of threads or processes doing a particular type of I/O action as specified by the user. fio takes a number of global parameters, each inherited by the thread unless otherwise parameters given to them overriding that setting is given. The typical use of fio is to write a job file matching the I/O load one wants to simulate."
+
+supported_releases:
+  - release:
+    version: "fio-3.36"
+    url: "https://github.com/axboe/fio/archive/refs/tags/fio-3.36.tar.gz"
+  - release:
+    version: "fio-3.35"
+    url: "https://github.com/axboe/fio/archive/refs/tags/fio-3.35.tar.gz"
+  - release:
+    version: "fio-3.34"
+    url: "https://github.com/axboe/fio/archive/refs/tags/fio-3.34.tar.gz"
+---
+
+<p>Fio</p>

_posts/2021-08-31-Flye.md

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+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "Flye"
+
+project:
+  title: "Flye"
+  type: "C"
+  url: "https://github.com/fenderglass/Flye"
+  project_official_url: "https://github.com/fenderglass/Flye"
+  logo: "/assets/images/projects/hpc/flye/logo.png"
+  overview: "Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies."
+
+supported_releases:
+  - release:
+    version: "2.9.2"
+    url: "https://github.com/fenderglass/Flye/archive/refs/tags/2.9.2.tar.gz"
+  - release:
+    version: "2.9.1"
+    url: "https://github.com/fenderglass/Flye/archive/refs/tags/2.9.1.tar.gz"
+  - release:
+    version: "2.9"
+    url: "https://github.com/fenderglass/Flye/archive/refs/tags/2.9.tar.gz"
+---
+
+<p>Flye</p>

_posts/2021-08-31-FreeSurfer.md

@@ -0,0 +1,29 @@
+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "FreeSurfer"
+
+project:
+  title: "FreeSurfer"
+  type: "C++"
+  url: "https://surfer.nmr.mgh.harvard.edu/"
+  project_official_url: "https://github.com/freesurfer/freesurfer"
+  logo: "/assets/images/projects/hpc/freesurfer/logo.png"
+  overview: "FreeSurfer is a software package for the analysis and visualization of neuroimaging data from cross-sectional and longitudinal studies."
+
+supported_releases:
+  - release:
+    version: "v7.4.1"
+    url: "https://github.com/freesurfer/freesurfer/tree/v7.4.1"
+  - release:
+    version: v7.4.0""
+    url: "https://github.com/freesurfer/freesurfer/tree/v7.4.0"
+  - release:
+    version: "v7.3.3"
+    url: "https://github.com/freesurfer/freesurfer/tree/v7.3.3"
+---
+
+<p>FreeSurfer</p>

_posts/2021-08-31-Jmeter.md

@@ -0,0 +1,29 @@
+---
+layout: project
+permalink: /:title/
+category: libraries
+
+meta:
+  keywords: "Jmeter"
+
+project:
+  title: "Jmeter"
+  type: "Java"
+  url: "https://jmeter.apache.org/"
+  project_official_url: "https://github.com/apache/jmeter"
+  logo: "/assets/images/projects/libraries/jmeter/logo.png"
+  overview: "The Apache JMeter™ application is open source software, a 100% pure Java application designed to load test functional behavior and measure performance. It was originally designed for testing Web Applications but has since expanded to other test functions.It can be used to simulate a heavy load on a server, group of servers, network or object to test its strength or to analyze overall performance under different load types."
+
+supported_releases:
+  - release:
+    version: "v5.6.1"
+    url: "https://github.com/apache/jmeter/archive/refs/tags/rel/v5.6.1.tar.gz"
+  - release:
+    version: "v5.6"
+    url: "https://github.com/apache/jmeter/archive/refs/tags/rel/v5.6.tar.gz"
+  - release:
+    version: "v5.5"
+    url: "https://github.com/apache/jmeter/archive/refs/tags/rel/v5.5.tar.gz"
+---
+
+<p>Jmeter</p>

_posts/2021-08-31-Juicer.md

@@ -0,0 +1,29 @@
+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "Juicer"
+
+project:
+  title: "Juicer"
+  type: "Shell"
+  url: "https://aidenlab.org/"
+  project_official_url: "https://github.com/aidenlab/juicer"
+  logo: "/assets/images/projects/hpc/juicer/logo.png"
+  overview: "Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps."
+
+supported_releases:
+  - release:
+    version: "1.6"
+    url: "https://github.com/aidenlab/juicer/archive/refs/tags/1.6.tar.gz"
+  - release:
+    version: "1.5.6"
+    url: "https://github.com/aidenlab/juicer/archive/refs/tags/1.5.6.tar.gz"
+  - release:
+    version: "1.5.5"
+    url: "https://github.com/aidenlab/juicer/archive/refs/tags/1.5.5.tar.gz"
+---
+
+<p>Juicer</p>

_posts/2021-08-31-LACHESIS.md

@@ -0,0 +1,23 @@
+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "LACHESIS"
+
+project:
+  title: "LACHESIS"
+  type: "C++"
+  url: "http://dx.doi.org/10.1038/nbt.2727"
+  project_official_url: "https://github.com/shendurelab/LACHESIS"
+  logo: "/assets/images/projects/hpc/lachesis/logo.png"
+  overview: "A software tool to measure the thread of life."
+
+supported_releases:
+  - release:
+    version: "master"
+    url: "https://github.com/shendurelab/LACHESIS/zipball/master"
+---
+
+<p>LACHESIS</p>

_posts/2021-08-31-Muscle.md

@@ -0,0 +1,23 @@
+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "Muscle"
+
+project:
+  title: "Muscle"
+  type: "C++"
+  url: "https://github.com/rcedgar/muscle"
+  project_official_url: "https://github.com/rcedgar/muscle"
+  logo: "/assets/images/projects/hpc/muscle/logo.png"
+  overview: "Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures."
+
+supported_releases:
+  - release:
+    version: "5.1"
+    url: "https://github.com/rcedgar/muscle/archive/refs/tags/v5.1.tar.gz"
+---
+
+<p>Muscle</p>

_posts/2021-08-31-RepeatMasker.md

@@ -0,0 +1,26 @@
+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "RepeatMasker"
+
+project:
+  title: "RepeatMasker"
+  type: "Perl"
+  url: "https://www.repeatmasker.org/"
+  project_official_url: "https://github.com/rmhubley/RepeatMasker"
+  logo: "/assets/images/projects/hpc/repeatmasker/logo.png"
+  overview: "RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked"
+
+supported_releases:
+  - release:
+    version: "4.1.5"
+    url: "https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.5.tar.gz"
+  - release:
+    version: "4.1.4"
+    url: "https://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.4.tar.gz"
+---
+
+<p>RepeatMasker</p>

_posts/2021-08-31-RepeatModeler.md

@@ -0,0 +1,29 @@
+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "RepeatModeler"
+
+project:
+  title: "RepeatModeler"
+  type: "Perl"
+  url: "https://github.com/Dfam-consortium/RepeatModeler"
+  project_official_url: "https://github.com/Dfam-consortium/RepeatModeler"
+  logo: "/assets/images/projects/hpc/repeatmodeler/logo.png"
+  overview: "RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data."
+
+supported_releases:
+  - release:
+    version: "2.0.5"
+    url: "https://github.com/Dfam-consortium/RepeatModeler/archive/refs/tags/2.0.5.tar.gz"
+  - release:
+    version: "2.0.4"
+    url: "https://github.com/Dfam-consortium/RepeatModeler/archive/refs/tags/2.0.4.tar.gz"
+  - release:
+    version: "2.0.3"
+    url: "https://github.com/Dfam-consortium/RepeatModeler/archive/refs/tags/2.0.3.tar.gz"
+---
+
+<p>RepeatModeler</p>

_posts/2021-08-31-TRF.md

@@ -0,0 +1,26 @@
+---
+layout: project
+permalink: /:title/
+category: hpc
+
+meta:
+  keywords: "TRF"
+
+project:
+  title: "TRF"
+  type: "C"
+  url: "https://tandem.bu.edu/trf/trf.html"
+  project_official_url: "https://github.com/Benson-Genomics-Lab/TRF"
+  logo: "/assets/images/projects/hpc/trf/logo.png"
+  overview: "A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences."
+
+supported_releases:
+  - release:
+    version: "v4.09.1"
+    url: "https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz"
+  - release:
+    version: "v4.09"
+    url: "https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.tar.gz"
+---
+
+<p>TRF</p>