wicopa issueshttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues2022-01-04T12:19:12Zhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/26Getting R packages does not work anymore2022-01-04T12:19:12ZremyGetting R packages does not work anymoreFor instance, entering "ape" in the list of package, does not return any result. Looking at the Web developer console, we can see:
```
getPackages.php?distrib=CRAN&filter=ape&patternName=true&patternDescription=true&limit=30
```For instance, entering "ape" in the list of package, does not return any result. Looking at the Web developer console, we can see:
```
getPackages.php?distrib=CRAN&filter=ape&patternName=true&patternDescription=true&limit=30
```https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/25Add a way to manage repositories directly from the admin panel2020-10-13T09:18:01ZremyAdd a way to manage repositories directly from the admin panelIt would be great to be able to add a new distro repository and the way to parse it directly from the admin panel.
In the same vein, we could think about a way to add a package specific repository (eg. : go, perl cpan ...).
Kind regard...It would be great to be able to add a new distro repository and the way to parse it directly from the admin panel.
In the same vein, we could think about a way to add a package specific repository (eg. : go, perl cpan ...).
Kind regards,
Rémyhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/24insert a cache in the dockerfile2020-05-07T06:56:53Zremyinsert a cache in the dockerfileIt would be nice to use either varnish or redis as a cache server in the dockerfile.It would be nice to use either varnish or redis as a cache server in the dockerfile.remyremyhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/23build command is wrong2020-05-12T13:14:51Zremybuild command is wrongThe build command indicated for both singularity and docker are bad. Indeed, for example, when you run "build command" for a singularity recipe, it lacks the definition filename.
For docker, you need a "-f" flag to indicate the file as ...The build command indicated for both singularity and docker are bad. Indeed, for example, when you run "build command" for a singularity recipe, it lacks the definition filename.
For docker, you need a "-f" flag to indicate the file as it can be another name than "Dockerfile" (maybe a "-t" flag to insert a label would be nice also).
Rémy.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/22adding a checkbox to add the right timezone and locales2020-03-23T14:32:45Zremyadding a checkbox to add the right timezone and localesIf you take a look at [this recipe](https://gitlab.mbb.univ-montp2.fr/mbb/singularity-local-recipes/blob/master/Singularity.basic-r-3.5.def) you will see that there is two sections to fix the timezone and the locales in the recipe. One i...If you take a look at [this recipe](https://gitlab.mbb.univ-montp2.fr/mbb/singularity-local-recipes/blob/master/Singularity.basic-r-3.5.def) you will see that there is two sections to fix the timezone and the locales in the recipe. One is generic; we should be able to add it easily:
```bash
# Timezone and locales settings
TZ=Europe/Paris
ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
#dpkg-reconfigure -f noninteractive tzdata
sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
locale-gen
echo 'LANG="en_US.UTF-8' >> /etc/default/locale
```
The other one is specific to R and is done later in the recipe:
```bash
## fixing locales in R
#echo 'LANG <- Sys.getenv("LANG")' | R --slave
#echo 'Sys.setlocale("LC_ALL", LANG)' | R --slave
```
This would be a nice enhancement in wicopajlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/21move the cluster added specific content to the end of the recipe2020-10-13T09:30:58Zremymove the cluster added specific content to the end of the recipeWe should move the admin cluster specific part to the end of the recipe.We should move the admin cluster specific part to the end of the recipe.https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/20R added automatically in every recipe2020-03-24T15:19:19ZremyR added automatically in every recipeI saw that R is installed each time in every recipe generation. That should be remove (or maybe just allowed with a check box to add manually this part in the recipe [\*]).
[\*] however, it is installed from sources with a `make` althou...I saw that R is installed each time in every recipe generation. That should be remove (or maybe just allowed with a check box to add manually this part in the recipe [\*]).
[\*] however, it is installed from sources with a `make` although the `make` program is not installed before...jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/19conda2020-10-12T10:06:29ZremycondaIssues with conda:
1. bioconda channel is not added by default (see [this issue on github](https://github.com/sylabs/singularity/issues/5094),
2. conda singularity recipes does not work when trying to run the image (build works but w...Issues with conda:
1. bioconda channel is not added by default (see [this issue on github](https://github.com/sylabs/singularity/issues/5094),
2. conda singularity recipes does not work when trying to run the image (build works but when running as a basic user (not root), conda is installed in /usr/local and singularity is trying to write into a tmp directory in /usr/local).
Maybe a more complex conda recipe would work: https://github.com/sylabs/singularity/issues/5075
Indeed, I think conda needs at least to create and initiate an environment.
Moreover, we could automate the runscript line to fit the conda installed program or add a `%app` dedicated section.https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/18apt update before installing packages2020-03-24T15:19:19Zremyapt update before installing packagesIf I am choosing to install distro packages, I am facing an issue due to the missing update part; eg:
```bash
apt install -y make
```
without any `apt update` before.If I am choosing to install distro packages, I am facing an issue due to the missing update part; eg:
```bash
apt install -y make
```
without any `apt update` before.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/17fedora and alpine distro2020-03-09T13:02:32Zremyfedora and alpine distroThe corresponding codes must be updated as these versions does not work anymore (current fedora is fedora 31 and the wicopa version is 29).The corresponding codes must be updated as these versions does not work anymore (current fedora is fedora 31 and the wicopa version is 29).jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/16R2020-03-24T15:19:19ZremyRCheck the R page which seems to be not working.Check the R page which seems to be not working.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/15Adding some sections like CMD or ENTRYPOINT / %runscript / %apprun2019-09-04T08:02:16ZremyAdding some sections like CMD or ENTRYPOINT / %runscript / %apprunIt should be possible to change the %runscript/ ENTRYPOINT without having to edit the recipe directly but by adding a section like the 'Tools' window in the main panel.
Indeed, we could have a 'Command to run' window that will replace `e...It should be possible to change the %runscript/ ENTRYPOINT without having to edit the recipe directly but by adding a section like the 'Tools' window in the main panel.
Indeed, we could have a 'Command to run' window that will replace `exec /bin/bash "$@"` (maybe by having a textbox with a preset value of `exec /bin/bash "$@"` that could be overwritten).
In the same vain, being able to add some `%apprun` or `CMD` sections would be nice too !
Rémy.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/14Recipe generation does not accept R None or empty version for R packages2019-05-27T13:55:25ZremyRecipe generation does not accept R None or empty version for R packagesThis can be an issue because we can import recipe from docker-hub (with images that already contain R) or install R from distro package.This can be an issue because we can import recipe from docker-hub (with images that already contain R) or install R from distro package.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/13CI / Build farm and personal git repository2019-05-08T16:35:52ZremyCI / Build farm and personal git repositoryMaybe the best thing to do to manage versions and history by recipe is to connect it to a personal github/gitlab repository. Then, the history of the recipe would be managed by Github or Gitlab itself.
So, it means that it would be nece...Maybe the best thing to do to manage versions and history by recipe is to connect it to a personal github/gitlab repository. Then, the history of the recipe would be managed by Github or Gitlab itself.
So, it means that it would be necessary to connect wicopa to these Git personal repositories with Github/Gitlab tokens.
Necessary stages:
- Associate Git(hub,lab) profile to wicopa personal user,
When creating an image:
- Create a recipe from wicopa,
- Save the recipe in wicopa database (recipe + metadatas (user, labels, tags, permissions...),
- push it to the personal git(hub,lab) repository,
- CI step here, using (travis/gitlab/circle)-ci ...,
- build the image.
This would be a bit complex, but that is what is ~ done on [singularity-hub](https://www.singularity-hub.org/). [Code is here](https://github.com/singularityhub/singularityhub.github.io)https://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/12rename "gestion"2019-05-20T13:06:30Zremyrename "gestion"Il faudrait que la partie "gestion" et toutes ses occurrences soient renommées en "Manage".
Du coup, la sous-partie "Gestion managers" deviendrait plutôt "Manage distribution packaging tools" puisque ça parle d'`apt`...Il faudrait que la partie "gestion" et toutes ses occurrences soient renommées en "Manage".
Du coup, la sous-partie "Gestion managers" deviendrait plutôt "Manage distribution packaging tools" puisque ça parle d'`apt`...jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/11Rajout de mots clés2019-06-21T09:28:46ZremyRajout de mots clésLa possibilité de stocker les recettes dans les historiques ( #10 ) pourrait permettre ultérieurement de faire des recherches dans les recettes, éventuellement avec des mots clés:
- Singularity: https://www.sylabs.io/guides/3.0/user-gu...La possibilité de stocker les recettes dans les historiques ( #10 ) pourrait permettre ultérieurement de faire des recherches dans les recettes, éventuellement avec des mots clés:
- Singularity: https://www.sylabs.io/guides/3.0/user-guide/environment_and_metadata.html
- Docker: https://docs.docker.com/engine/reference/builder/#label
On pourrait envisager une recherche découpée ainsi:
- Recherches par mot-clés de type tags/labels dans la recette
- dans mon historique
- dans l'historique publique
- Recherches dans l'ensemble de la recette
- dans mon historique
- dans l'historique publique
Avec éventuellement un nuage de mot clés permettant de trouver des recettes plus rapidement en fonction des mots clés les plus utilisés, sans même rechercher.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/10Historique et partage2020-10-12T09:11:30ZremyHistorique et partageEn se basant sur #9 , nous pourrions stocker dans une base historique qui ferait le lien avec une table user, le contenu des recettes déjà générées. Par ailleurs, on pourrait rajouter un flag pour savoir si la recette est publique (parta...En se basant sur #9 , nous pourrions stocker dans une base historique qui ferait le lien avec une table user, le contenu des recettes déjà générées. Par ailleurs, on pourrait rajouter un flag pour savoir si la recette est publique (partagée avec tout le monde) ou pas, ou voir avec un groupe en particulier (nécessite la création/gestion de groupe; peut-être pas utile au départ).jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/9Authentification2020-10-12T09:06:27ZremyAuthentificationUne gestion des authentification avec un plugin LDAP/OAuth permettrait aux utilisateurs de se connecter.
L'idée est de pouvoir implémenter de nouvelles fonctionnalités basées sur le profil de l'utilisateur et ses habitudes.Une gestion des authentification avec un plugin LDAP/OAuth permettrait aux utilisateurs de se connecter.
L'idée est de pouvoir implémenter de nouvelles fonctionnalités basées sur le profil de l'utilisateur et ses habitudes.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/8Chemin absolu dans wicopa2019-04-10T11:21:36ZremyChemin absolu dans wicopaJ'ai repéré des chemins absolus (notamment dans la page de login) qui fait que si wicopa n'est pas installé dans `$DOCUMENT_ROOT/wicopa`, le lien ne fonctionnera pas.J'ai repéré des chemins absolus (notamment dans la page de login) qui fait que si wicopa n'est pas installé dans `$DOCUMENT_ROOT/wicopa`, le lien ne fonctionnera pas.jlopezjlopezhttps://gitlab.mbb.univ-montp2.fr/jlopez/wicopa/-/issues/7cluster specific configuration2019-07-19T09:28:08Zremycluster specific configurationL'idée serait d'avoir une checkbox dans le panneau de construction de la recette qui permettrait à un administrateur de cluster de rajouter automatiquement dans la section de son choix une liste de commandes bash à exécuter, pour rendre ...L'idée serait d'avoir une checkbox dans le panneau de construction de la recette qui permettrait à un administrateur de cluster de rajouter automatiquement dans la section de son choix une liste de commandes bash à exécuter, pour rendre la recette compatible avec un environnement de cluster local.
Ceci pourrait se faire depuis le panneau d'administration.
Par exemple, admettons qu'on souhaite monter un scratch, il faudra que le dossier existe sur le conteneur avant de le monter, si on veut rajouter un utilisateur système, créer des liens symboliques ou changer des variables d'environnement, rajouter OpenMPI qui match la version sur le cluster... Bref, des choses que savent faire et connaissent les administrateurs de cluster qui se mettra généralement en section `%post` de singularity avec écriture des variables d'environnements dans /.singularity/...jlopezjlopez