Mercurial > repos > galaxy-australia > alphafold2

annotate README.rst @ 13:c0e71cb2bd1b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 830b5bbf9c5375e714e1b7b9a3e8eec1e584e6b2
author galaxy-australia
date Wed, 12 Oct 2022 22:25:20 +0000
parents 7fbec959cf2b
children d00e15139065
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
1 Alphafold compute setup
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
2 =======================
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
3
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
4 Overview
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
5 --------
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
6
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
7 Alphafold requires a customised compute environment to run. The machine
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
8 needs a GPU, and access to a 2.2 Tb reference data store.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
9
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
10 This document is designed to provide details on the compute environment
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
11 required for Alphafold operation, and the Galaxy job destination
8
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
12 settings to run the wrapper. We strongly suggest reading this entire document
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
13 to ensure that your setup is compatible with the hardware that you are
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
14 deploying to.
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
15
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
16 For full details on Alphafold requirements, see
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
17 https://github.com/deepmind/alphafold.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
18
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
19 HARDWARE
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
20 ~~~~~~~~
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
21
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
22 The machine is recommended to have the following specs: - 12 cores - 80
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
23 Gb RAM - 2.5 Tb storage - A fast Nvidia GPU.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
24
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
25 As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
26 **unified memory** to be switched on. Unified memory is usually enabled
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
27 by default, but some HPC systems will turn it off so the GPU can be
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
28 shared between multiple jobs concurrently.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
29
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
30 ENVIRONMENT
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
31 ~~~~~~~~~~~
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
32
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
33 This wrapper runs Alphafold as a singularity container. The following
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
34 software are needed:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
35
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
36 - `Singularity <https://sylabs.io/guides/3.0/user-guide/installation.html>`_
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
37 - `NVIDIA Container
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
38 Toolkit <https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html>`_
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
39
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
40 As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
41 This makes the GPU available inside the running singularity container.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
42
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
43 To check that everything has been set up correctly, run the following
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
44
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
45 ::
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
46
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
47 singularity run --nv docker://nvidia/cuda:11.0-base nvidia-smi
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
48
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
49 If you can see something similar to this output (details depend on your
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
50 GPU), it has been set up correctly.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
51
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
52 ::
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
53
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
54 +-----------------------------------------------------------------------------+
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
55 | NVIDIA-SMI 470.57.02 Driver Version: 470.57.02 CUDA Version: 11.4 |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
56 |-------------------------------+----------------------+----------------------+
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
57 | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
58 | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
59 | | | MIG M. |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
60 |===============================+======================+======================|
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
61 | 0 Tesla T4 Off | 00000000:00:05.0 Off | 0 |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
62 | N/A 49C P0 28W / 70W | 0MiB / 15109MiB | 0% Default |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
63 | | | N/A |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
64 +-------------------------------+----------------------+----------------------+
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
65
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
66 +-----------------------------------------------------------------------------+
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
67 | Processes: |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
68 | GPU GI CI PID Type Process name GPU Memory |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
69 | ID ID Usage |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
70 |=============================================================================|
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
71 | No running processes found |
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
72 +-----------------------------------------------------------------------------+
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
73
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
74 REFERENCE DATA
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
75 ~~~~~~~~~~~~~~
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
76
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
77 Alphafold needs reference data to run. The wrapper expects this data to
11
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
78 be present at ``/data/alphafold_databases``. A custom DB root can be read from
2
abba603c6ef3 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
galaxy-australia
parents: 1
diff changeset
79 the ALPHAFOLD_DB environment variable, if set. To download the AlphaFold,
abba603c6ef3 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86-dirty"
galaxy-australia
parents: 1
diff changeset
80 reference data, run the following shell script command in the tool directory.
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
81
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
82 ::
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
83
11
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
84 # Set databases root
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
85 ALPHAFOLD_DB_ROOT=/data/alphafold_databases
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
86
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
87 # make folders if needed
11
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
88 mkdir -p $ALPHAFOLD_DB_ROOT
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
89
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
90 # download ref data
11
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
91 bash scripts/download_all_data.sh $ALPHAFOLD_DB_ROOT
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
92
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
93 This will install the reference data to ``/data/alphafold_databases``.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
94 To check this has worked, ensure the final folder structure is as
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
95 follows:
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
96
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
97 ::
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
98
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
99 data/alphafold_databases
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
100 ├── bfd
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
101 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
102 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
103 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
104 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
105 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
106 │   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
107 ├── mgnify
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
108 │   └── mgy_clusters_2018_12.fa
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
109 ├── params
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
110 │   ├── LICENSE
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
111 │   ├── params_model_1.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
112 │   ├── params_model_1_ptm.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
113 │   ├── params_model_2.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
114 │   ├── params_model_2_ptm.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
115 │   ├── params_model_3.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
116 │   ├── params_model_3_ptm.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
117 │   ├── params_model_4.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
118 │   ├── params_model_4_ptm.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
119 │   ├── params_model_5.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
120 │   └── params_model_5_ptm.npz
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
121 ├── pdb70
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
122 │   ├── md5sum
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
123 │   ├── pdb70_a3m.ffdata
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
124 │   ├── pdb70_a3m.ffindex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
125 │   ├── pdb70_clu.tsv
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
126 │   ├── pdb70_cs219.ffdata
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
127 │   ├── pdb70_cs219.ffindex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
128 │   ├── pdb70_hhm.ffdata
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
129 │   ├── pdb70_hhm.ffindex
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
130 │   └── pdb_filter.dat
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
131 ├── pdb_mmcif
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
132 │   ├── mmcif_files
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
133 │   └── obsolete.dat
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
134 ├── uniclust30
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
135 │   └── uniclust30_2018_08
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
136 └── uniref90
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
137 └── uniref90.fasta
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
138
11
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
139 In more recent releases of the AlphaFold tool, you will need to download an
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
140 additional file to allow the ``reduced_dbs`` option:
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
141
12
7fbec959cf2b planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 6fdbb269efd97b6f5c6ab40db4ab0b23459f884b
galaxy-australia
parents: 11
diff changeset
142 ::
7fbec959cf2b planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 6fdbb269efd97b6f5c6ab40db4ab0b23459f884b
galaxy-australia
parents: 11
diff changeset
143
11
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
144 bash scripts/download_small_bfd.sh $ALPHAFOLD_DB_ROOT
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
145
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
146 The ``$ALPHAFOLD_DB_ROOT`` directory should now contain this additional file:
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
147
12
7fbec959cf2b planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 6fdbb269efd97b6f5c6ab40db4ab0b23459f884b
galaxy-australia
parents: 11
diff changeset
148 ::
7fbec959cf2b planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 6fdbb269efd97b6f5c6ab40db4ab0b23459f884b
galaxy-australia
parents: 11
diff changeset
149
11
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
150 data/alphafold_databases
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
151 ├── small_bfd
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
152 │   └── bfd-first_non_consensus_sequences.fasta
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
153
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
154
81d1ef460bb3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
galaxy-australia
parents: 8
diff changeset
155
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
156 JOB DESTINATION
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
157 ~~~~~~~~~~~~~~~
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
158
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
159 Alphafold needs a custom singularity job destination to run. The
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
160 destination needs to be configured for singularity, and some extra
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
161 singularity params need to be set as seen below.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
162
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
163 Specify the job runner. For example, a local runner
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
164
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
165 ::
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
166
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
167 <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
168
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
169 Customise the job destination with required singularity settings. The
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
170 settings below are mandatory, but you may include other settings as
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
171 needed.
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
172
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
173 ::
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
174
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
175 <destination id="alphafold" runner="alphafold_runner">
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
176 <param id="dependency_resolution">'none'</param>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
177 <param id="singularity_enabled">true</param>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
178 <param id="singularity_run_extra_arguments">--nv</param>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
179 <param id="singularity_volumes">"$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro"</param>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
180 </destination>
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
181
7
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
parents: 2
diff changeset
182 CUSTOM PARAMETERS
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
parents: 2
diff changeset
183 ~~~~~~~~~~~~~~~~~
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
parents: 2
diff changeset
184
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
parents: 2
diff changeset
185 A few parameters can be customized with the use of environment variables set in the job destination:
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
parents: 2
diff changeset
186
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
parents: 2
diff changeset
187 - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``)
8
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
188 - ``ALPHAFOLD_USE_GPU [True/False]``: set to ``False`` to disable GPU dependency (defaults to ``True``)
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
189 - ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``0``)
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
190 - ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``0`` - no validation)
7
eb085b3dbaf8 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
galaxy-australia
parents: 2
diff changeset
191
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
192 Closing
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
193 ~~~~~~~
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
194
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
195 If you are experiencing technical issues, feel free to write to
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
196 help@genome.edu.au. We may be able to provide advice on setting up
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff changeset
197 Alphafold on your compute environment.