From 8930fd89902aaf4b1bbd2e2cb35116ea982aaac2 Mon Sep 17 00:00:00 2001 From: Sergey Venev Date: Tue, 18 Dec 2018 18:53:30 -0500 Subject: [PATCH 1/6] explain forking and reference other sources --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index ef3fb74..6dde7c7 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,8 @@ +# pacbio assembly + +We are stealing this to combine with this [gist](https://gist.github.com/audy/26748bdf6f5e260dd6f6) to create a usable Pacbio assembly pipeline with their web-interface. + + # renseq Renseq Pacbio pipeline From 5d04f2dc9935e11456cd498b83d60f8941a75846 Mon Sep 17 00:00:00 2001 From: sergpolly Date: Tue, 18 Dec 2018 19:10:20 -0500 Subject: [PATCH 2/6] a working version with some docs --- Dockerfile | 4 +++- README.md | 11 +++++++++++ scripts/runrun.sh | 13 +++++++++++++ 3 files changed, 27 insertions(+), 1 deletion(-) create mode 100755 scripts/runrun.sh diff --git a/Dockerfile b/Dockerfile index 8cb58dc..603ce8d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,4 +35,6 @@ RUN usermod -d /tmp nobody USER admin -ENTRYPOINT ["/home/admin/scripts/runRenSeq.sh"] +EXPOSE 8080 + +ENTRYPOINT ["/home/admin/scripts/runrun.sh"] diff --git a/README.md b/README.md index 6dde7c7..ec7642d 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,17 @@ We are stealing this to combine with this [gist](https://gist.github.com/audy/26748bdf6f5e260dd6f6) to create a usable Pacbio assembly pipeline with their web-interface. +1. build an image: +`docker build -t pacbio .` +2. run it, exposing port and mounting volums: +`docker run -dit -p 8080:8080 --volume /data:/data --name pacbio-container pacbio` +semantics: +`docker run -dit -p outside:inside --volume outside:inside --name pacbio-container pacbio` +3. browse running container if you need to: +`docker exec -it pacbio-container /bin/bash` +4. access it in the browser: +`localhost:8080`, `localhost:${outside}`, `${hostname}:8080` or , `${hostname}:${outside}`, where `${}` are placeholders ment to be replaced with the corresponding values. + # renseq Renseq Pacbio pipeline diff --git a/scripts/runrun.sh b/scripts/runrun.sh new file mode 100755 index 0000000..595214d --- /dev/null +++ b/scripts/runrun.sh @@ -0,0 +1,13 @@ +#!/bin/bash +set -euo pipefail + +# adopted from +# https://gist.github.com/audy/26748bdf6f5e260dd6f6 + +# runs as daemon in background +/opt/smrtanalysis/admin/bin/smrtportald-initd start + +# sleep forever to prevent container from exiting +while sleep 1000; do + echo "hello" +done From af917d480af9a72a8e053b579a883f727bd3c905 Mon Sep 17 00:00:00 2001 From: Sergey Venev Date: Tue, 18 Dec 2018 19:28:03 -0500 Subject: [PATCH 3/6] found a way to contribute instead of keeping fork contribute an alternative entrypoint - the rest could be take care of by the `docker run` options --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index ec7642d..9093f7c 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,14 @@ semantics: 4. access it in the browser: `localhost:8080`, `localhost:${outside}`, `${hostname}:8080` or , `${hostname}:${outside}`, where `${}` are placeholders ment to be replaced with the corresponding values. +## notes and todo-s: + +1. seems like we could have overwritten entrypoint with `docker run --entrypoint sript/runrun.sh` +2. same goes for exposing ports: `docker run --expose 8080` +3. 1 and 2 imply that could have just contributed to the original repo by adding a dummy `runrun.sh` and providing some instructions on how to achieve a running web-interface ... +4. try doing it + + # renseq Renseq Pacbio pipeline From 5de13ce81abcc7325222608a7c8f517341475eb1 Mon Sep 17 00:00:00 2001 From: sergpolly Date: Tue, 17 Sep 2019 11:06:00 -0400 Subject: [PATCH 4/6] update to minimal change ready to PRA --- Dockerfile | 7 +++--- README.md | 42 +++++++++++++------------------- scripts/{runrun.sh => runWeb.sh} | 0 3 files changed, 21 insertions(+), 28 deletions(-) rename scripts/{runrun.sh => runWeb.sh} (100%) diff --git a/Dockerfile b/Dockerfile index 603ce8d..7229709 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,6 +35,7 @@ RUN usermod -d /tmp nobody USER admin -EXPOSE 8080 - -ENTRYPOINT ["/home/admin/scripts/runrun.sh"] +# # following could be provided as flags to "docker run" +# # to be removed once functionality has been confirmed: +# EXPOSE 8080 +# ENTRYPOINT ["/home/admin/scripts/runrun.sh"] diff --git a/README.md b/README.md index 9093f7c..454b429 100644 --- a/README.md +++ b/README.md @@ -1,35 +1,27 @@ -# pacbio assembly - -We are stealing this to combine with this [gist](https://gist.github.com/audy/26748bdf6f5e260dd6f6) to create a usable Pacbio assembly pipeline with their web-interface. - -1. build an image: -`docker build -t pacbio .` -2. run it, exposing port and mounting volums: -`docker run -dit -p 8080:8080 --volume /data:/data --name pacbio-container pacbio` -semantics: -`docker run -dit -p outside:inside --volume outside:inside --name pacbio-container pacbio` -3. browse running container if you need to: -`docker exec -it pacbio-container /bin/bash` -4. access it in the browser: -`localhost:8080`, `localhost:${outside}`, `${hostname}:8080` or , `${hostname}:${outside}`, where `${}` are placeholders ment to be replaced with the corresponding values. - -## notes and todo-s: - -1. seems like we could have overwritten entrypoint with `docker run --entrypoint sript/runrun.sh` -2. same goes for exposing ports: `docker run --expose 8080` -3. 1 and 2 imply that could have just contributed to the original repo by adding a dummy `runrun.sh` and providing some instructions on how to achieve a running web-interface ... -4. try doing it - - - # renseq Renseq Pacbio pipeline ![Docker infoimage badge](https://img.shields.io/badge/ImageInfo-_5.584_GB/_25_Layers_-blue.svg?style=flat-square) -Apologies for the size of this image, but it installs the entire PACBio SMRT-Analysis suite which is quite big. And apparently, to run the CLI `smrtpipe.py`, [the whole suite *must* be installed](https://github.com/PacificBiosciences/SMRT-Analysis/issues/256), including a mysqldb and a full web stack for a web GUI that is never used. Anyway, most of the bulk seem to be folders mysteriously named "parameters" with a date. Gigs worth of parameters, why not? +Apologies for the size of this image, but it installs the entire PACBio SMRT-Analysis suite which is quite big. And apparently, to run the CLI `smrtpipe.py`, [the whole suite *must* be installed](https://github.com/PacificBiosciences/SMRT-Analysis/issues/256), including a mysqldb and a full web stack for a web GUI that is never used (read). Anyway, most of the bulk seem to be folders mysteriously named "parameters" with a date. Gigs worth of parameters, why not? + +Combining this docker image with the entrypoint from the following [gist](https://gist.github.com/audy/26748bdf6f5e260dd6f6), one can run the fully functional web-interface of the PacBio assembly pipeline. ## Usage + +1. `renseq` pipeline: + put your files in a folder that will be mounted in the image as a volume e.g. `data`. Then: `docker run -ti -v data:/home/admin/data cyverseuk/renseq /home/admin/data/adapter.fasta /home/admin/data/file1.h5 /home/admin/data/file2.h5 etc...` + +2. web-interface for PacBio assembly pipeline: + +run this docker exposing port, mounting volumes and providing alternative entrypoint: +`docker run -dit --entrypoint ./scripts/runWeb.sh --expose 8080 -p 8080:8080 --volume /data:/data --name pacbio-container pacbio` +semantics: + +3. general docker tips: + - building this image: `docker build -t pacbio .` + - ports and volumes mapping semantics: `--port outside_port:inside_port --volume outside_path:inside_path` + - to access running web-interface in the browser go to: `0.0.0.0:outside_port` or `your_hostname:outside_port` diff --git a/scripts/runrun.sh b/scripts/runWeb.sh similarity index 100% rename from scripts/runrun.sh rename to scripts/runWeb.sh From c96993da45ad948fbd8432ce90fa023793ef3ba5 Mon Sep 17 00:00:00 2001 From: sergpolly Date: Tue, 17 Sep 2019 11:20:39 -0400 Subject: [PATCH 5/6] revert dockerfile to original --- Dockerfile | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7229709..18daa64 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,7 +35,4 @@ RUN usermod -d /tmp nobody USER admin -# # following could be provided as flags to "docker run" -# # to be removed once functionality has been confirmed: -# EXPOSE 8080 -# ENTRYPOINT ["/home/admin/scripts/runrun.sh"] +ENTRYPOINT ["/home/admin/scripts/runRenSeq.sh"] \ No newline at end of file From 9a2dc36b427960edbb12639e8a5647a27ee70483 Mon Sep 17 00:00:00 2001 From: sergpolly Date: Tue, 17 Sep 2019 11:24:05 -0400 Subject: [PATCH 6/6] cleanup --- Dockerfile | 2 +- README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 18daa64..8cb58dc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,4 +35,4 @@ RUN usermod -d /tmp nobody USER admin -ENTRYPOINT ["/home/admin/scripts/runRenSeq.sh"] \ No newline at end of file +ENTRYPOINT ["/home/admin/scripts/runRenSeq.sh"] diff --git a/README.md b/README.md index 454b429..f208ff5 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ Renseq Pacbio pipeline ![Docker infoimage badge](https://img.shields.io/badge/ImageInfo-_5.584_GB/_25_Layers_-blue.svg?style=flat-square) -Apologies for the size of this image, but it installs the entire PACBio SMRT-Analysis suite which is quite big. And apparently, to run the CLI `smrtpipe.py`, [the whole suite *must* be installed](https://github.com/PacificBiosciences/SMRT-Analysis/issues/256), including a mysqldb and a full web stack for a web GUI that is never used (read). Anyway, most of the bulk seem to be folders mysteriously named "parameters" with a date. Gigs worth of parameters, why not? +Apologies for the size of this image, but it installs the entire PACBio SMRT-Analysis suite which is quite big. And apparently, to run the CLI `smrtpipe.py`, [the whole suite *must* be installed](https://github.com/PacificBiosciences/SMRT-Analysis/issues/256), including a mysqldb and a full web stack for a web GUI that is never used (read below if it is really needed). Anyway, most of the bulk seem to be folders mysteriously named "parameters" with a date. Gigs worth of parameters, why not? Combining this docker image with the entrypoint from the following [gist](https://gist.github.com/audy/26748bdf6f5e260dd6f6), one can run the fully functional web-interface of the PacBio assembly pipeline.