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updating link to puppet #2

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a99b465
Added structure 5A8E
viis Sep 30, 2015
f84565f
Removed extra text in meetings page
viis Oct 2, 2015
1705fd9
Updated protein files and added a cache dir
viis Oct 5, 2015
7f00229
Removed ligand data. Ligand data is now stored in the cache dir in a …
viis Oct 6, 2015
9130c74
Added a sphinx generated docs directory as a test
viis Oct 7, 2015
424dc61
Updated docs config
viis Oct 7, 2015
8a9d328
Added dummy pages
viis Oct 7, 2015
107685e
Added more dummy pages to demonstrate the structure of the docs
viis Oct 8, 2015
67349a3
Updated documentation pages
viis Oct 10, 2015
12ae265
Added docs text for web services
viis Oct 10, 2015
d9edaf0
Updated developer docs
viis Oct 10, 2015
e023643
Added a sites page to the docs
viis Oct 11, 2015
6105797
Updated meetings page in docs
viis Oct 15, 2015
ffeee52
Updated meetings page in docs
viis Oct 15, 2015
a4f71fb
Added docs pages for receptors and external servers
viis Oct 16, 2015
a2e3698
Updated docs about PDB file numbering.
viis Oct 16, 2015
c621fb8
Updated structure annotations
viis Oct 16, 2015
29795f1
Removed documentation and pages, these are now a part of the external…
viis Oct 19, 2015
43c85fc
Updated errors on acknowledgements page
viis Oct 20, 2015
9273642
Updated errors on acknowledgements page
viis Oct 20, 2015
2d15254
Merged gpcr/gpcrdb_data into master
cmunk Oct 21, 2015
f402771
It should be 4x58 instead of 4x48. I believe it was a typo
pszgaspar Oct 26, 2015
5337022
Merged in pszgaspar/gpcrdb_data (pull request #15)
viis Oct 27, 2015
37c8fc6
Merged gpcr/gpcrdb_data into master
pszgaspar Oct 27, 2015
51d8a2d
I think the correct annotation is in construct 4XNW. This is definite…
pszgaspar Oct 27, 2015
f286599
Merge branch 'master' of https://bitbucket.org/pszgaspar/gpcrdb_data
pszgaspar Oct 27, 2015
1c73a15
1U19 misses bulge 5x461 and constriction 4x59 I think.
pszgaspar Oct 27, 2015
7ae75e1
fix
pszgaspar Oct 28, 2015
85dbefe
Merged in pszgaspar/gpcrdb_data (pull request #16)
viis Oct 28, 2015
b353e61
Updates segments, generic numbers, anomalies and reference positions …
viis Oct 29, 2015
9804d40
Merge branch 'master' of bitbucket.org:gpcr/gpcrdb_data
viis Oct 29, 2015
e3b3352
Updated 3VW7 structure annotation
viis Oct 31, 2015
440895e
Added minimum length to loop segments
viis Nov 2, 2015
f1baf10
Updated minimum loop length
viis Nov 4, 2015
dace80b
Fixed error in structure 4PHU
viis Nov 4, 2015
8ed8597
Removed receptor entries from protein file
viis Nov 4, 2015
2f7be1d
Updated mutations site in docs
viis Nov 6, 2015
b4b6784
Updated link in docs
viis Nov 6, 2015
ba459b1
Updated docs
viis Nov 7, 2015
30aa340
Updated format of construct data files
viis Nov 20, 2015
3c6fb46
Added a documentation page on building a local database
viis Nov 20, 2015
d5b039d
Updated docs pages on reloading and building a database
viis Nov 24, 2015
06756ac
Added a tutorial to documentation
viis Dec 1, 2015
afb1ca0
Added a video to the tutorial, and added questions to the Receptors p…
viis Dec 2, 2015
59bfac5
Added questions to tutorial in docs
viis Dec 2, 2015
3ae32b6
Updated reference positions for GPR143
viis Dec 10, 2015
e2fa1f8
Merged gpcr/gpcrdb_data into master
cmunk Jan 6, 2016
a92b68a
Update to mutant data.
cmunk Jan 6, 2016
541508f
Merged in chrmunk/gpcrdb_data (pull request #17)
viis Jan 6, 2016
718c40e
Updated structure file format to add segment borders for modeling, an…
viis Jan 11, 2016
028bd68
Ligand info for 4O9R and 4OR2
cmunk Jan 15, 2016
b84bb6d
Revert "Ligand info for 4O9R and 4OR2"
cmunk Jan 15, 2016
d7c9531
Merged gpcr/gpcrdb_data into master
cmunk Jan 15, 2016
cee84b3
Updated ligand info for 4OR2 and 4O9R
cmunk Jan 15, 2016
ee4a7b4
Merged in chrmunk/gpcrdb_data (pull request #18)
viis Jan 15, 2016
4fe18e3
4OR2.yaml annotation updates for ICL1-3
kharpsoe Jan 20, 2016
9c20565
4OO9.yaml structural annotation updates
kharpsoe Jan 20, 2016
f22caa1
5CGC.yaml, new mGlu5 structure added
kharpsoe Jan 20, 2016
b420f37
5CGD.yaml, new mGlu5 structure added
kharpsoe Jan 20, 2016
2c29b98
5CGC.yaml, new mGlu5 structure added
kharpsoe Jan 20, 2016
f9c3cda
5CGC.yaml format update
kharpsoe Jan 20, 2016
8192bf5
5CGD.yaml, new mGlu5 structure added
kharpsoe Jan 20, 2016
23f2c2d
Created README.md
viis Jan 21, 2016
7752b84
Updated docs for local installations
viis Jan 21, 2016
cd96bb2
Updated links to GitHub in docs for local installation
viis Jan 21, 2016
fe989b7
Added 2016 NAR paper to citation page in docs
viis Jan 21, 2016
9d76579
Changed Bitbucket links to GitHub
viis Jan 21, 2016
c9badfb
Fixed typo in docs index
viis Jan 21, 2016
064dc65
Updated Uniprot code for A3 receptor
viis Jan 21, 2016
32bf4d8
Updated paths for loading a database in docs
viis Jan 25, 2016
4b4bdc2
Testing webhooks
viis Jan 25, 2016
6118c04
Updated proteins and families from IUPHAR
AlexanderHauser Jan 25, 2016
8ccac60
Merge pull request #1 from AlexanderHauser/master
viis Jan 25, 2016
645c210
Added Glisten Erlangen to meetings page
viis Jan 27, 2016
d487fa0
Merge branch 'master' of github.com:protwis/gpcrdb_data
viis Jan 27, 2016
2d846d5
Alignment updates
AlexanderHauser Jan 29, 2016
17e3af6
Merge pull request #2 from AlexanderHauser/master
viis Jan 29, 2016
893e690
Proteins and families fix
AlexanderHauser Jan 29, 2016
331cfd3
Merge pull request #3 from AlexanderHauser/master
viis Jan 29, 2016
67b37b6
Updated reference positions for ICL1 and H8
viis Jan 29, 2016
dc21700
Fixed error in proteins and family file
viis Jan 29, 2016
583dcdb
Added loop generic numbers to classes B, C, and F
viis Jan 29, 2016
ed8a8a4
Update of 23.50 and 45.50 positions
kharpsoe Feb 9, 2016
86f0b5c
Merge pull request #4 from kharpsoe/patch-1
cmunk Feb 9, 2016
865cbf8
Updated 1x50 position in v1br_human
kharpsoe Feb 9, 2016
3af0fe2
Merge pull request #1 from protwis/master
cmunk Feb 9, 2016
4a67b64
Merge pull request #6 from cmunk/master
cmunk Feb 9, 2016
b60bfc0
Added loop generic numbers to sequence based schemes
viis Feb 14, 2016
d8d1ec3
Specify chain of peptide ligand
cmunk Feb 19, 2016
550474b
Merge pull request #7 from cmunk/master
cmunk Feb 19, 2016
528d22a
small fixes in structure_segment_modeling entries
pszgaspar Mar 16, 2016
6b976a5
Changing segments_in_structure values so it is the same as in David's…
pszgaspar Mar 21, 2016
a3deead
Merge pull request #8 from pszgaspar/master
viis Mar 22, 2016
3fbd680
Merge pull request #5 from kharpsoe/patch-2
viis Mar 22, 2016
43a5d6b
Added generic number 23x54
viis Mar 22, 2016
41c320d
Added 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
6e97dbc
Added/updated 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
93fa1e6
Added/updated 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
768bdf4
Added/updated 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
4bc815d
Added/updated 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
7e4d8ba
Added/updated 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
f81d299
Added/updated 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
2ae3936
Added/updated 50-position for ICL1 and H8
kharpsoe Mar 30, 2016
87dca9e
Merge commit '2ae3936cc405de6165ac31d1c450aea28205cf81'
Mar 30, 2016
0881262
Merge commit 'f81d299e8cc41806a88f85fed0a584870388ab5e'
Mar 30, 2016
4a5cc82
Merge commit '7e4d8bac1023a0bb9e51bb6392cbf8d8ad5479c9'
Mar 30, 2016
e6505c6
Merge commit '4bc815d28f2eff1fc424797949a5d4038a7fd175'
Mar 30, 2016
098e73f
Merge commit '768bdf4ac1c2b0990b7f9b34edbc62ca7b8210e1'
Mar 30, 2016
08f1af7
Merge commit '93fa1e6a2e429a5a5beb595633c6788e17913cef'
Mar 30, 2016
d5b5b03
Merge commit '6e97dbc3d0ba2704afe532a953eff416c2541b76'
Mar 30, 2016
627af45
Merge pull request #9 from kharpsoe/master
cmunk Mar 30, 2016
82aa46e
correction
pszgaspar Apr 3, 2016
59893ca
correction
pszgaspar Apr 3, 2016
d5c4a92
correction
pszgaspar Apr 3, 2016
4a89814
alignment updates
AlexanderHauser Apr 4, 2016
81d46a8
New mutant data (5HT is new, and rest are updated to newest format)
cmunk Apr 4, 2016
4da0757
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
cmunk Apr 4, 2016
2140b79
Merge pull request #12 from cmunk/master
cmunk Apr 4, 2016
28e69ac
Added 8x50 annotation to many non class A receptors
viis Apr 6, 2016
49402d1
Addition of 8x50 and update of 12x50 of all class C receptors, except…
Apr 11, 2016
11327ba
Merge pull request #10 from pszgaspar/master
viis Apr 16, 2016
e0c9345
Resolved conflicts in class C reference positions
Apr 18, 2016
857ec15
Class C updates
Apr 18, 2016
6244062
Non class C Helix 8
Apr 18, 2016
28316ae
return of vipr2 (undelation)
Apr 18, 2016
1286d02
Merge pull request #13 from kharpsoe/master
viis Apr 18, 2016
ddc4f16
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
AlexanderHauser Apr 18, 2016
b6c436c
conflicts sorted
AlexanderHauser Apr 18, 2016
8d69f03
Merge pull request #11 from AlexanderHauser/master
viis Apr 19, 2016
24acd80
Updated structure annotations
viis Apr 19, 2016
d84f929
Removed anomaly in 4EIY
viis Apr 24, 2016
9998081
Added a numbering scheme to Taste 2 receptors
viis Apr 24, 2016
b69bb9d
Fixed incorrect PDB code in 4BOU structure
viis Apr 25, 2016
45da780
wrong HETCODE for 2Y01.
cmunk Apr 26, 2016
f511cdc
Merge pull request #14 from cmunk/master
cmunk Apr 26, 2016
f24f493
first g protein data
cmunk Apr 26, 2016
fbf8520
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
cmunk Apr 26, 2016
d0afd8f
Merge pull request #15 from cmunk/master
cmunk Apr 26, 2016
d55bf03
Updated class structure files
viis Apr 27, 2016
8c86e4f
Alignment updates
AlexanderHauser May 4, 2016
3f2d12f
Merge pull request #16 from AlexanderHauser/master
viis May 5, 2016
17f786a
Added structure annotations from David
viis May 6, 2016
ccb005c
Added quotation marks around - in reference position files
viis May 6, 2016
af8ffd6
Added position 12x52 to relevant numbering schemes
viis May 7, 2016
d728573
Updated 8x50 positions in ADRB1 and ADRB2
viis May 7, 2016
ddeaf8c
Removed bulges in loop in structures 2YDV and 3REY
viis May 8, 2016
1100f19
Alignment refinement
AlexanderHauser May 10, 2016
620a4cc
Merge pull request #17 from AlexanderHauser/master
viis May 10, 2016
53e838a
Alignment refinement
AlexanderHauser May 13, 2016
6b1aa11
Merge pull request #18 from AlexanderHauser/master
viis May 14, 2016
5307ba7
Updated structure annotations
viis May 14, 2016
23b4d1e
Updated structure files and added constructs for missing structures
viis May 14, 2016
b2e7add
Added release notes for 2016-05-18
viis May 15, 2016
b54f888
Adding missing non-representative structures
pszgaspar May 26, 2016
318b9da
correction
pszgaspar May 26, 2016
a465afe
fix
pszgaspar May 29, 2016
df3a50f
Merge pull request #19 from pszgaspar/master
viis Jun 9, 2016
81d5181
Update citing.rst
davidgloriam Jun 21, 2016
6f59b00
Change to V2R human
Jul 5, 2016
20d1cb5
Merge pull request #20 from kharpsoe/master
cmunk Jul 5, 2016
59fdf91
first construct_data
cmunk Jul 6, 2016
349ca44
CGN data from Madan Babus group to incorporate in GPCRdb
AlexanderHauser Jul 19, 2016
afb73b7
New G protein selectivity dataset
AlexanderHauser Jul 19, 2016
a573238
New mutation data from Chris
cmunk Jul 20, 2016
9eacf19
Extending TM1 and H8 for Class B1 and B2
pszgaspar Jul 21, 2016
fff41f1
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
AlexanderHauser Jul 25, 2016
2e577f8
Update citing.rst with Mutation Design Tool paper
cmunk Aug 2, 2016
9f5d09e
Added drug data
AlexanderHauser Aug 8, 2016
390ed99
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
AlexanderHauser Aug 8, 2016
5ebdb27
Davids Annotation excel
cmunk Aug 23, 2016
855f6a8
new excel annotation commit
cmunk Sep 11, 2016
b3ba7a4
annotation update
cmunk Sep 11, 2016
7d09504
small annotation fix
cmunk Sep 12, 2016
166a49d
annotation fix
cmunk Sep 12, 2016
313c34e
annotation fix
cmunk Sep 12, 2016
b39bf38
latest annotation fix, primarily 4x58
cmunk Sep 13, 2016
8364246
Added CaSR mutants from Leach 2016
Sep 14, 2016
0f68fc4
fix GN scheme mapping file
cmunk Sep 14, 2016
9fca56d
more mapping fix
cmunk Sep 14, 2016
4f9ca0e
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
pszgaspar Sep 14, 2016
3478f49
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
pszgaspar Sep 14, 2016
a5e7707
5GLI, 5GLH
pszgaspar Sep 14, 2016
45b4307
Merge pull request #22 from pszgaspar/master
cmunk Sep 14, 2016
f49843c
fix
pszgaspar Sep 14, 2016
ae3cd52
fix
pszgaspar Sep 14, 2016
0981879
specify chain in 3 peptide xtals
cmunk Sep 14, 2016
ea975ea
Merge pull request #23 from pszgaspar/master
cmunk Sep 14, 2016
288564a
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
cmunk Sep 14, 2016
f6a765c
fix ligand info for 5GLH
cmunk Sep 15, 2016
1b16fc5
fix a mutation to 0 (zero) in chemokine set
cmunk Sep 16, 2016
7fc23a4
4BOU to 4BUO in annotations
cmunk Sep 19, 2016
e7d278a
Updated drug data
AlexanderHauser Sep 20, 2016
6044f67
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
AlexanderHauser Sep 20, 2016
4bca002
update drug data FDA approval years
AlexanderHauser Sep 20, 2016
e55578c
Update drug data
AlexanderHauser Sep 20, 2016
c2c74e5
new release notes
cmunk Sep 21, 2016
10461cc
update to alignments (primarily xtal annotation)
cmunk Oct 3, 2016
ed6216c
Update mutations.rst
cmunk Oct 7, 2016
081d2bc
Updated G protein data for G13 in human
AlexanderHauser Oct 10, 2016
2aa5843
Updated Drug data
AlexanderHauser Oct 10, 2016
286f801
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
AlexanderHauser Oct 12, 2016
46b9d9e
New mutant data on A2A, ednr and CB2
Oct 13, 2016
598ba57
Merge branch 'master' of https://github.com/kharpsoe/gpcrdb_data
cmunk Oct 13, 2016
3fa6d83
Fix for CB2 and secretin-like mutants from Chris Graaf
cmunk Oct 13, 2016
95dd930
Corrections to CB2 mutants and the submission from Anke
Oct 13, 2016
dae8097
Merge branch 'master' of https://github.com/kharpsoe/gpcrdb_data
cmunk Oct 14, 2016
391d829
Release note update links
AlexanderHauser Oct 14, 2016
951f836
Adhesion family reclassification
AlexanderHauser Oct 24, 2016
131a121
Fix states of several structures
cmunk Oct 26, 2016
efa89c0
Merge branch 'master' of https://github.com/AlexanderHauser/gpcrdb_data
cmunk Oct 27, 2016
032d8fa
Indication corrected and updated dataset
AlexanderHauser Oct 28, 2016
6912f1a
Removed old dataset
AlexanderHauser Oct 28, 2016
68ea1cf
termo mutants for construct tool
cmunk Oct 31, 2016
6c88f9e
Changes to gp179 and gp158 in helix 4 and 5 in regards to x50
cmunk Nov 10, 2016
720116f
new xtals
pszgaspar Nov 16, 2016
8bd4ea3
Data update Gprotein pairing
AlexanderHauser Nov 17, 2016
5a28f56
Merge pull request #24 from pszgaspar/master
cmunk Nov 18, 2016
07fb73e
G protein barcode data
AlexanderHauser Nov 23, 2016
6396dce
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
AlexanderHauser Nov 23, 2016
b46a1cc
updated excel
pszgaspar Nov 23, 2016
697a2b9
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
pszgaspar Nov 23, 2016
1044b87
Merge pull request #25 from pszgaspar/master
cmunk Nov 23, 2016
7626c82
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
cmunk Nov 23, 2016
a3f4f9e
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
pszgaspar Nov 23, 2016
bba1673
cnr1_human added
cmunk Nov 23, 2016
8d30147
Merge branch 'master' of https://github.com/AlexanderHauser/gpcrdb_data
cmunk Nov 23, 2016
0ec0ec0
new construct data
cmunk Nov 28, 2016
2d7c145
GLP1R mutant data
cmunk Nov 30, 2016
4a1be16
remove wrong mutant file
cmunk Nov 30, 2016
26edf84
structure rules (for construct design tool)
cmunk Nov 30, 2016
b8cd7da
Merge branch 'master' of https://github.com/protwis/gpcrdb_data
pszgaspar Dec 8, 2016
fcba006
5IU8 fix
pszgaspar Dec 8, 2016
da64ab1
Merge branch 'master' of https://github.com/pszgaspar/gpcrdb_data
Feb 1, 2017
b1591be
cleanup
Feb 1, 2017
86915b9
updating link to puppet repo
May 2, 2017
bcadf79
updating puppet link
May 2, 2017
3c36c87
updating link to puppet
May 2, 2017
2802f3f
readme
May 2, 2017
ce38371
readme
May 2, 2017
dbd8dc3
readme
May 2, 2017
824c83b
updating link to submodule
May 10, 2017
220847e
Updated puppet modules commit
cmunk Sep 6, 2017
c5ff515
Merge branch 'master' of https://github.com/protwis/protwis_vagrant
cmunk Sep 6, 2017
d148c21
update vagrant modules
cmunk Sep 6, 2017
56a4a2b
Change from ubuntu 14.04 to 18.04 -- requires disksize increase to 20…
cmunk Jan 9, 2020
a64b243
Update README.md
cmunk Jan 9, 2020
61b4937
submodule update
pszgaspar Feb 11, 2020
0557b12
Revert "submodule update"
pszgaspar Feb 11, 2020
99a3330
puppet updates
pszgaspar Feb 11, 2020
1c4ba84
Merge branch 'master' of https://github.com/pszgaspar/protwis_vagrant
pszgaspar Feb 11, 2020
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6 changes: 6 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,12 @@ Clone into the "shared" directory (replace your-username with your GitHub userna
cd ~/protwis_vagrant
git clone https://github.com/your-username/protwis.git shared/sites/protwis

##### Add vagrant plugin

This allows for VM boxes to change disk size

vagrant plugin install vagrant-disksize

##### Start the vagrant box

This may take a few minutes
Expand Down
8 changes: 5 additions & 3 deletions Vagrantfile
Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
Vagrant.configure("2") do |config|

# Vagrant box to build off of.
config.vm.box = "ubuntu/trusty64"
config.vm.box = "ubuntu/bionic64"
config.disksize.size = '20GB'

# Forward ports
config.vm.network :forwarded_port, guest: 22, host: 2226, id: "ssh"
Expand All @@ -11,15 +12,16 @@ Vagrant.configure("2") do |config|
# Allocate resources
config.vm.provider :virtualbox do |vb|
vb.customize ["modifyvm", :id, "--ioapic", "on"]
vb.customize ["modifyvm", :id, "--memory", "1024"]
vb.customize ["modifyvm", :id, "--cpus", "2"]
vb.customize ["modifyvm", :id, "--memory", "4096"]
vb.customize ["modifyvm", :id, "--cpus", "4"]
end

# Set up a shared directory
config.vm.synced_folder "shared", "/protwis/", :owner => "vagrant"

# copy puppet scripts to VM
config.vm.provision "file", source: "protwis_puppet_modules", destination: "/protwis/conf/protwis_puppet_modules"
config.vm.provision "shell", inline: "sudo apt-get update && sudo apt-get install -y puppet"

# Enable the Puppet provisioner
config.vm.provision :puppet do |puppet|
Expand Down