tamuanand · tamuanand · May 2, 2023 · May 2, 2023 · May 3, 2023 · May 5, 2023
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -16,22 +16,24 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install python dependencies
       run: |
-        python -m pip install galaxy-tool-util
+        python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/util
+        python -m pip install git+https://git@github.com/galaxyproject/galaxy.git@dev#subdirectory=packages/tool_util
+        #python -m pip install galaxy-tool-util
     - run: docker --version
     - run: docker info
     - name: Build images
       run: |
-        mulled-build-files --check-published --singularity --namespace $MULLED_NAMESPACE build-and-test ./combinations --verbose
+        mulled-build-files --check-published --singularity --namespace $MULLED_NAMESPACE --use-mamba  build-and-test ./combinations --verbose
     - name: Upload images (if pushed to master branch)
       if: github.ref == 'refs/heads/master' && github.repository_owner == 'BioContainers'
       env:
         SSH_AUTH_SOCK: /tmp/ssh_agent.sock
         INVOLUCRO_AUTH: "https://${{ secrets.MY_USER }}:${{ secrets.MY_PASSWORD }}@quay.io/v1/?email=${{ secrets.MY_EMAIL }}"
       run: |
          mkdir -p ~/.ssh
-         ssh-keyscan -t rsa orval.galaxyproject.org >> ~/.ssh/known_hosts
+         ssh-keyscan -t rsa depot.galaxyproject.org >> ~/.ssh/known_hosts
          ssh-agent -a $SSH_AUTH_SOCK > /dev/null
          ssh-add - <<< "${{ secrets.ORVAL_KEY }}"
          mulled-build-files --check-published --namespace $MULLED_NAMESPACE --oauth-token ${{ secrets.QUAY_OAUTH_TOKEN }} push ./combinations
          ls -l singularity_import
-         [ "$(ls -A singularity_import)" ] && echo 'uploading Singularity images' && scp singularity_import/*:* singularity@orval.galaxyproject.org:/srv/nginx/depot.galaxyproject.org/root/singularity/
+         [ "$(ls -A singularity_import)" ] && echo 'uploading Singularity images' && scp singularity_import/*:* singularity@depot.galaxyproject.org:/srv/nginx/depot.galaxyproject.org/root/singularity/
diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 ## Building multiple package Containers
 
 Creating containers is easy! All you need to do is add a combination of packages to the
-[hash.tsv file](https://github.com/BioContainers/multi-package-containers/blob/master/combinations/hash.tsv).
+[hash.tsv file](/combinations/hash.tsv).
 
 To assemble the required string of package combinations you can use the little
 [helper service](https://biocontainers.pro/#/multipackage) 
@@ -15,14 +15,54 @@ Singularity images hosted at https://depot.galaxyproject.org/singularity/ (Hosti
 ## Associated command line tools
 
 You can list and search for existing conda packages and container images as well as build multi-package container images locally 
-using the command line `mulled-*` tools avialable as part of [`galaxy-tool-util`](https://pypi.org/project/galaxy-tool-util/) 
+using the command line `mulled-*` tools available as part of [`galaxy-tool-util`](https://pypi.org/project/galaxy-tool-util/), which source
+code is hosted as part of the [Galaxy repo](https://github.com/galaxyproject/galaxy/tree/dev/lib/galaxy/tool_util/).
 These can be installed using conda 
 
 ```
 conda create -n mulled galaxy-tool-util -c conda-forge -c bioconda
 conda activate mulled
 ```
 
+## Searching for containers
+
+Multi-tool containers have hashed names to make them uniquely identifiable.
+You usually don't search for containers you construct the hash and pull them down. However, if you have the need to search for them, we have a CLI tool
+that helps you.
+
+```
+(planemo) bag@bag:~$ mulled-search --destination quay singularity -s deeptools samtools
+The query returned the following result(s).
+LOCATION     NAME                                                VERSION                                     COMMAND
+quay         samtools                                            1.3.1--4                                    docker pull quay.io/biocontainers/samtools:1.3.1--4
+quay         samtools                                            1.3.1--3                                    docker pull quay.io/biocontainers/samtools:1.3.1--3
+quay         samtools                                            1.3.1--2                                    docker pull quay.io/biocontainers/samtools:1.3.1--2
+quay         samtools                                            1.0--0                                      docker pull quay.io/biocontainers/samtools:1.0--0
+quay         samtools                                            1.3--1                                      docker pull quay.io/biocontainers/samtools:1.3--1
+...
+singularity  deeptools                                           3.4.2--py_0                                 wget https://depot.galaxyproject.org/singularity/deeptools:3.4.2--py_0
+singularity  deeptools                                           3.4.3--py_0                                 wget https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0
+singularity  deeptools                                           3.5.0--py_0                                 wget https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0
+singularity  deeptools                                           3.5.1--py_0                                 wget https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0
+singularity  deeptools                                           3.5.1--pyhdfd78af_1                         wget https://depot.galaxyproject.org/singularity/deeptools:3.5.1--pyhdfd78af_1
+singularity  deeptools                                           3.5.2--pyhdfd78af_0                         wget https://depot.galaxyproject.org/singularity/deeptools:3.5.2--pyhdfd78af_0
+...
+singularity  samtools                                            1.9--h8571acd_10                            wget https://depot.galaxyproject.org/singularity/samtools:1.9--h8571acd_10
+singularity  samtools                                            1.9--h8571acd_11                            wget https://depot.galaxyproject.org/singularity/samtools:1.9--h8571acd_11
+singularity  samtools                                            1.9--h8ee4bcc_1                             wget https://depot.galaxyproject.org/singularity/samtools:1.9--h8ee4bcc_1
+singularity  samtools                                            1.9--h91753b0_2                             wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_2
+singularity  samtools                                            1.9--h91753b0_3                             wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_3
+singularity  samtools                                            1.9--h91753b0_4                             wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_4
+singularity  samtools                                            1.9--h91753b0_5                             wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_5
+singularity  samtools                                            1.9--h91753b0_8                             wget https://depot.galaxyproject.org/singularity/samtools:1.9--h91753b0_8
+...
+singularity  mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a  9796fae7f3dc33539425911572b1af41da23d71c-0  wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:9796fae7f3dc33539425911572b1af41da23d71c-0
+singularity  mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a  b7b2dac42861f5ad3a6dcbf1626378de27694869-0  wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:b7b2dac42861f5ad3a6dcbf1626378de27694869-0
+singularity  mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a  d4ca6cb58c17558e45d789d552f8d20c2f0cf912-0  wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:d4ca6cb58c17558e45d789d552f8d20c2f0cf912-0
+singularity  mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a  d67d021ff194d58c15cca934dd3dfe948d1c7145-0  wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:d67d021ff194d58c15cca934dd3dfe948d1c7145-0
+singularity  mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a  e4be5f66213daef5a53e2a179b7e0c1d22016afe-0  wget https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:e4be5f66213daef5a53e2a179b7e0c1d22016afe-0
+```
+
 ## Setting up such a repository
 
  - Fork this repository or copy the [github workflow](https://github.com/BioContainers/multi-package-containers/blob/master/.github/workflows/ci.yaml).

diff --git a/combinations/10x_bamtofastq:1.4.1-0.tsv b/combinations/10x_bamtofastq:1.4.1-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+10x_bamtofastq=1.4.1	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/bandage_ng:2022.09-0.tsv b/combinations/bandage_ng:2022.09-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+bandage_ng=2022.09	quay.io/bioconda/base-glibc-debian-bash:latest	0
diff --git a/combinations/binning_refiner:1.4.3-0.tsv b/combinations/binning_refiner:1.4.3-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+binning_refiner=1.4.3	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/bioconductor-dada2:1.28-0.tsv b/combinations/bioconductor-dada2:1.28-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+bioconductor-dada2=1.28	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/biom-format:2.1.10-0.tsv b/combinations/biom-format:2.1.10-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+biom-format=2.1.10	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/biom-format:2.1.12-0.tsv b/combinations/biom-format:2.1.12-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+biom-format=2.1.12	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/biom-format:2.1.13-0.tsv b/combinations/biom-format:2.1.13-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+biom-format=2.1.13	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/biom-format:2.1.14-0.tsv b/combinations/biom-format:2.1.14-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+biom-format=2.1.14	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/biopython:1.75-0.tsv b/combinations/biopython:1.75-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+biopython=1.75	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/cdo:2.0.0-0.tsv b/combinations/cdo:2.0.0-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+cdo=2.0.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/cherri:0.7-0.tsv b/combinations/cherri:0.7-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+cherri=0.7	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/chopin2:1.0.7-0.tsv b/combinations/chopin2:1.0.7-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+chopin2=1.0.7	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/cif2cell:2.0.0a3-0.tsv b/combinations/cif2cell:2.0.0a3-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+cif2cell=2.0.0a3	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/coverm-0.tsv b/combinations/coverm-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+coverm	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/curl:7.80.0-0.tsv b/combinations/curl:7.80.0-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+curl=7.80.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/datamash:1.8-0.tsv b/combinations/datamash:1.8-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+datamash=1.8	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/dnabot:3.1.0-0.tsv b/combinations/dnabot:3.1.0-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+dnabot=3.1.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/doebase:2.0.2-0.tsv b/combinations/doebase:2.0.2-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+doebase=2.0.2	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/doebase:v2.0.2-0.tsv b/combinations/doebase:v2.0.2-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+doebase=v2.0.2	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/fastpca:0.9.1-0.tsv b/combinations/fastpca:0.9.1-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+fastpca=0.9.1	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/fpocket:4.0.0-0.tsv b/combinations/fpocket:4.0.0-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+fpocket=4.0.0	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/gromacs:2022-0.tsv b/combinations/gromacs:2022-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+gromacs=2022	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/gzip:1.11-0.tsv b/combinations/gzip:1.11-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+gzip=1.11	quay.io/bioconda/base-glibc-busybox-bash:latest	0
diff --git a/combinations/hapog:1.3.3-0.tsv b/combinations/hapog:1.3.3-0.tsv
@@ -0,0 +1,2 @@
+#targets	base_image	image_build
+hapog=1.3.3	quay.io/bioconda/base-glibc-busybox-bash:latest	0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		10x_bamtofastq=1.4.1 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		bandage_ng=2022.09 quay.io/bioconda/base-glibc-debian-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		binning_refiner=1.4.3 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		bioconductor-dada2=1.28 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		biom-format=2.1.10 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		biom-format=2.1.12 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		biom-format=2.1.13 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		biom-format=2.1.14 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		biopython=1.75 quay.io/bioconda/base-glibc-busybox-bash:latest 0
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		#targets base_image image_build
		cdo=2.0.0 quay.io/bioconda/base-glibc-busybox-bash:latest 0