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update visium tutorials
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@davehorsfall
davehorsfall committed May 10, 2023
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Expand Up @@ -29,7 +29,18 @@ Make a copy of the WebAtlas repo and change directory into the new repo:
git clone git@github.com:haniffalab/webatlas-pipeline.git
cd webatlas-pipeline
.. code-block:: shell
:caption: Output
Cloning into 'webatlas-pipeline'...
remote: Enumerating objects: 1966, done.
remote: Counting objects: 100% (341/341), done.
remote: Compressing objects: 100% (144/144), done.
remote: Total 1966 (delta 227), reused 204 (delta 195), pack-reused 1625
Receiving objects: 100% (1966/1966), 5.78 MiB | 5.91 MiB/s, done.
Resolving deltas: 100% (1292/1292), done.
**#3. Check java is installed**

Make sure java 11 later is installed on your computer by using the command:
Expand All @@ -38,7 +49,13 @@ Make sure java 11 later is installed on your computer by using the command:
:caption: Input
java -version
openjdk version "11"
.. code-block:: shell
:caption: Output
openjdk version "11.0.18" 2023-01-17
OpenJDK Runtime Environment (build 11.0.18+10-post-Ubuntu-0ubuntu120.04.1)
OpenJDK 64-Bit Server VM (build 11.0.18+10-post-Ubuntu-0ubuntu120.04.1, mixed mode, sharing)
**#4. Install Nextflow**

Expand All @@ -49,6 +66,24 @@ Enter this command in your terminal to install nextflow in the current directory
curl -s https://get.nextflow.io | bash
.. code-block:: shell
:caption: Output
CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.5.1
...
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:23.04.1
N E X T F L O W
version 23.04.1 build 5866
created 15-04-2023 06:51 UTC (07:51 BST)
cite doi:10.1038/nbt.3820
http://nextflow.io
Nextflow installation completed. Please note:
- the executable file `nextflow` has been created in the folder: ./webatlas-pipeline
- you may complete the installation by moving it to a directory in your $PATH
**#5. Check Docker is installed**

Make sure Docker Engine 20.10 later is installed on your computer by using the command:
Expand All @@ -62,6 +97,13 @@ Make sure Docker Engine 20.10 later is installed on your computer by using the c
:caption: Output
Client: Docker Engine - Community
Version: 23.0.4
API version: 1.42
Go version: go1.19.8
Git commit: f480fb1
Built: Fri Apr 14 10:32:23 2023
OS/Arch: linux/amd64
Context: default
**#6. Build the docker images**

Expand All @@ -75,49 +117,143 @@ Make sure Docker Engine 20.10 later is installed on your computer by using the c
.. code-block:: shell
:caption: Output
somet
[+] Building 152.0s (9/9) FINISHED
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 874B 0.0s
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load metadata for docker.io/library/python:3.9 1.7s
=> [1/4] FROM docker.io/library/python:3.9@sha256:6ea9dafc96d7914c5c1d199f1f0195c4e05cf017b10666ca84cb7ce8e2699d51 26.9s
=> => resolve docker.io/library/python:3.9@sha256:6ea9dafc96d7914c5c1d199f1f0195c4e05cf017b10666ca84cb7ce8e2699d51 0.0s
=> => sha256:4eedd9c5abf7e5f63753a5e788cb0872a715fa1141e8ce5ea87638e6cd370a41 54.58MB / 54.58MB 11.3s
=> => sha256:6ea9dafc96d7914c5c1d199f1f0195c4e05cf017b10666ca84cb7ce8e2699d51 1.86kB / 1.86kB 0.0s
=> => sha256:c65dadac8789fed40962578392e99a0528dcb868442c75d144e68ba858984837 2.01kB / 2.01kB 0.0s
=> => sha256:27ac39eccd1fd7d6c7f78eefc98233e633a7178dd05910983ba905ecf71561f3 7.51kB / 7.51kB 0.0s
=> => sha256:5d79063a01c561833dc6546d4e647fda0121a59e1a9a17874a3e30854555475e 15.76MB / 15.76MB 3.0s
=> => sha256:918547b9432687b1e1d238e82dc1e0ea0b736aafbf3c402eea98c6db81a9cb65 55.05MB / 55.05MB 6.5s
=> => sha256:9cdadd40055fb82fef74a0a38f29fb1ee7b6922e18370ebdc3502ec66f79fa3f 196.85MB / 196.85MB 22.0s
=> => sha256:2a12d0031f3fc457f41eaa0e29c0eaf4ba1376735aa940268ebccc76abb49f04 6.29MB / 6.29MB 8.7s
=> => extracting sha256:918547b9432687b1e1d238e82dc1e0ea0b736aafbf3c402eea98c6db81a9cb65 0.7s
=> => extracting sha256:5d79063a01c561833dc6546d4e647fda0121a59e1a9a17874a3e30854555475e 0.2s
=> => sha256:cea461a97d8717d5ef1eb563adaf205de17b9bf5b9bd57bc6bb2eae2296a8740 16.15MB / 16.15MB 11.9s
=> => extracting sha256:4eedd9c5abf7e5f63753a5e788cb0872a715fa1141e8ce5ea87638e6cd370a41 1.5s
=> => sha256:a48c72dfa8c4e0da323ce32dac703c79d8f2de134e6a420cdfbc868323cfc68a 244B / 244B 12.0s
=> => sha256:c343b921680a19bf22934b83c02f42d8fdd0d8559417f63c1dcd2d7997c22da3 2.90MB / 2.90MB 12.6s
=> => extracting sha256:9cdadd40055fb82fef74a0a38f29fb1ee7b6922e18370ebdc3502ec66f79fa3f 2.9s
=> => extracting sha256:2a12d0031f3fc457f41eaa0e29c0eaf4ba1376735aa940268ebccc76abb49f04 0.2s
=> => extracting sha256:cea461a97d8717d5ef1eb563adaf205de17b9bf5b9bd57bc6bb2eae2296a8740 0.3s
=> => extracting sha256:a48c72dfa8c4e0da323ce32dac703c79d8f2de134e6a420cdfbc868323cfc68a 0.0s
=> => extracting sha256:c343b921680a19bf22934b83c02f42d8fdd0d8559417f63c1dcd2d7997c22da3 0.1s
=> [internal] load build context 0.0s
=> => transferring context: 736B 0.0s
=> [2/4] COPY ./requirements.txt /requirements.txt 0.8s
=> [3/4] RUN apt-get update && apt-get install -y --no-install-recommends wget unzip cmake g++ ant procps libblosc1 lib 27.6s
=> [4/4] RUN pip install --upgrade pip setuptools distlib --no-cache-dir && pip install --no-cache-dir -r /requirements.txt 91.3s
=> exporting to image 3.7s
=> => exporting layers 3.7s
=> => writing image sha256:71bf0c89267114ae8df748dfd8d262c253f7cd2658c2221d329e50604cab1722 0.0s
=> => naming to docker.io/haniffalab/webatlas-pipeline:0.0.1
**#7. Download and extract the sample data**

.. code-block:: shell
:caption: Input
wget https://www.something.com/WSSS_THYst9699525.tar.gz
mkdir -p ./input/WSSS_THYst9699525
tar -xzvf WSSS_THYst9699525.tar.gz -C ./input/WSSS_THYst9699525
.. code-block:: shell
:caption: Output
./
./WSSS_THYst9699525.h5ad
./WSSS_THYst9699525.yaml
./S3364_C59-FLEG-FO1_C1_HnE-2020-10-07-10.08.32.tif
**#7. Download the data**
**#8. Run the pipeline**

.. code-block:: shell
:caption: Input
wget https://www.something.com
tar ...
nextflow run main.nf -params-file input/WSSS_THYst9699525/WSSS_THYst9699525.yaml -entry Full_pipeline
.. code-block:: shell
:caption: Output
dgdf
N E X T F L O W ~ version 22.10.6
Launching `main.nf` [intergalactic_tuckerman] DSL2 - revision: 903c9797fa
executor > local (7)
executor > local (7)
[42/8000d9] process > Full_pipeline:Process_files:route_file (h5ad, WSSS_THYst9699525.h5ad) [100%] 1 of 1 ✔
[fa/e7a593] process > Full_pipeline:Process_images:Generate_image ([lowerlimb, visium-WSSS_THYst9699525], l... [100%] 1 of 1 ✔
[42/2a6dab] process > Full_pipeline:Process_images:image_to_zarr (S3364_C59-FLEG-FO1_C1_HnE-2020-10-07-10.0... [100%] 2 of 2 ✔
[4e/59100f] process > Full_pipeline:Process_images:ome_zarr_metadata (METADATA.ome.xml) [100%] 2 of 2 ✔
[58/0f5162] process > Full_pipeline:Output_to_config:Build_config ([lowerlimb, visium-WSSS_THYst9699525]) [100%] 1 of 1 ✔
lowerlimb-visium-WSSS_THYst9699525-anndata.zarr
{"dimOrder": "XYZCT", "channel_names": [], "X": "15040", "Y": "26680", "Z": "1", "C": "1", "T": "1"}
**#8. Download the input configuration file**
{"dimOrder": "XYZCT", "channel_names": [], "X": "15040", "Y": "26680", "Z": "1", "C": "3", "T": "1"}
**#9. Check execution was successful**
The output from the pipeline will indicate if the execution was successful. You can also
verify the expected directories are created.
.. code-block:: shell
:caption: Input
wget https://www.something.com
tar ...
ls -l ./output/WSSS_THYst9699525/0.0.1
.. code-block:: shell
:caption: Output
dgdf
drwxrwxr-x 11 dave dave 4096 May 10 11:35 lowerlimb-WSSS_THYst9699525-anndata.zarr
-rw-r--r-- 1 dave dave 5104 May 10 11:36 lowerlimb-WSSS_THYst9699525-config.json
-rw-r--r-- 1 dave dave 802534656 May 10 11:35 lowerlimb-WSSS_THYst9699525-label.tif
drwxrwxr-x 4 dave dave 4096 May 10 11:35 lowerlimb-WSSS_THYst9699525-label.zarr
drwxrwxr-x 4 dave dave 4096 May 10 11:36 lowerlimb-WSSS_THYst9699525-raw.zarr
**#9. Run the pipeline**
**#10. Serve the data output through a local web server**
To browse and explore the data, you need to serve the output data through a web server.
You can use your preferred web server, but you must ensure the data is served over port 3000,
at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-Origin header.
.. code-block:: shell
:caption: Input
nextflow run main.nf -params-file visium.yaml -entry Full_pipeline
npx http-server ./output/WSSS_THYst9699525/0.0.1 --port 3000 --cors
.. code-block:: shell
:caption: Output
dgdf
Starting up http-server, serving ./
http-server version: 14.1.1
http-server settings:
CORS: true
Cache: 3600 seconds
Connection Timeout: 120 seconds
Directory Listings: visible
AutoIndex: visible
Serve GZIP Files: false
Serve Brotli Files: false
Default File Extension: none
**#10. Check execution was successful**
Available on:
http://127.0.0.1:3000
http://192.168.0.23:3000
Hit CTRL-C to stop the server
**#11. Serve the data output through a web browser**
**#11. Explore data in your browser**
**#12. Load data in your browser**
Start your web browser and open:
https://webatlas.cog.sanger.ac.uk/dev/index.html?theme=dark&config=http://127.0.0.1:8080/lowerlimb-visium-WSSS_THYst9699525-config.json

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