Merge pull request #37 from neherlab/feat/add-fasttree

## add fasttree to docker - added `fasttree` to docker. - added `fasttree` binary download in `bin/setup-pangraph`. - updated list of dependencies in docs
neherlab · Oct 13, 2022 · 25ada6a · 25ada6a
2 parents a238679 + 5d3b1c3
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@
 - fixed a bug in detransitive, see this [commit](https://github.com/neherlab/pangraph/commit/a9651323aba2822d1b1c380a086fae4216c8030d)
 - added snakemake pipeline in the `script` folder to perform the analysis published in our [paper](https://github.com/neherlab/pangraph#citing).
 - added `-K` option to the `build` command to control kmer length for mmseqs aligner, see this [commit](https://github.com/neherlab/pangraph/commit/0857c36c7c8d11d53e8efab91cf5d18c35685a6e).
+- added `fasttree` to docker container and PanX export to docker tests, see [#37](https://github.com/neherlab/pangraph/pull/37).
 
 ## v0.5.0
 

diff --git a/Dockerfile b/Dockerfile
@@ -14,7 +14,6 @@ RUN set -euxo pipefail \
   curl \
   mafft \
   make \
-  mash \
   >/dev/null \
   && apt-get autoremove --yes >/dev/null \
   && apt-get clean autoclean >/dev/null \
@@ -59,6 +58,7 @@ RUN set -euxo pipefail \
   && apt-get install -qq --no-install-recommends --yes \
   mafft \
   mash \
+  fasttree \
   >/dev/null \
   && apt-get autoremove --yes >/dev/null \
   && apt-get clean autoclean >/dev/null \

diff --git a/README.md b/README.md
@@ -77,8 +77,8 @@ Moreover, for the compilation to work, it is necessary to have [MAFFT](https://m
 
 ### Optional dependencies
 
-**pangraph** can _optionally_ use [mash](https://github.com/marbl/Mash), [MAFFT](https://mafft.cbrc.jp/alignment/software/) or [mmseqs2](https://github.com/soedinglab/MMseqs2), as explained in [the documentation](https://neherlab.github.io/pangraph/#Optional-dependencies).
-For full functionality, it is recommended to install these tools and have them available on `$PATH`.
+**pangraph** can _optionally_ use [mash](https://github.com/marbl/Mash), [MAFFT](https://mafft.cbrc.jp/alignment/software/), [mmseqs2](https://github.com/soedinglab/MMseqs2) or [fasttree](http://www.microbesonline.org/fasttree/) for some optional functionalities, as explained in [the documentation](https://neherlab.github.io/pangraph/#Optional-dependencies).
+For use of these functionalities, it is recommended to install these tools and have them available on `$PATH`.
 
 Alternatively, a script `bin/setup-pangraph` is provided to install both tools into `bin/` for Linux-based operating systems.
 

diff --git a/bin/setup-pangraph b/bin/setup-pangraph
@@ -33,6 +33,18 @@ downloadMMseqs()
     mv "$name/bin/$name" "../bin/$name"
 }
 
+downloadFasttree()
+{
+    name="$1"; shift 1
+    url="$1";  shift 1
+
+    cd $root
+
+    curl -L -o "$name" "$url"
+    chmod +x "$name"
+    mv "$name" "../bin/$name"
+}
+
 build()
 {
     name="$1"; shift 1
@@ -55,5 +67,6 @@ build()
 
 (downloadMash "mash" "https://github.com/marbl/Mash/releases/download" "v2.2" "Linux64")
 (downloadMMseqs "mmseqs" "https://github.com/soedinglab/MMseqs2/releases/download" "13-45111" "sse2" "linux")
+(downloadFasttree "fasttree" "http://www.microbesonline.org/fasttree/FastTree")
 (build "mafft" "https://mafft.cbrc.jp/alignment/software" "7.490")
 # rm -r $root
diff --git a/docs/src/cli/export.md b/docs/src/cli/export.md
@@ -4,21 +4,21 @@
 Export a pangraph to a chosen file format(s)
 
 ## Options
-| Name                | Type    | Short Flag | Long Flag           | Description                                                                       |
-| :------------------ | :------ | :--------- | :------------------ | :-------------------------------------------------------------------------------- |
-| Edge minimum length | Integer | ell        | edge-minimum-length | blocks below this length cutoff will be ignored for edges in graph                |
-| Edge maximum length | Integer | elu        | edge-maximum-length | blocks above this length cutoff will be ignored for edges in graph                |
-| Edge minimum depth  | Integer | edl        | edge-minimum-depth  | blocks below this depth cutoff will be ignored for edges in graph                 |
-| Edge maximum depth  | Integer | edu        | edge-maximum-depth  | blocks above this depth cutoff will be ignored for edges in graph                 |
-| Minimum length      | Integer | ll         | minimum-length      | blocks below this length cutoff will be ignored for export                        |
-| Maximum length      | Integer | lu         | maximum-length      | blocks above this length cutoff will be ignored for export                        |
-| Minimum depth       | Integer | dl         | minimum-depth       | blocks below this depth cutoff will be ignored for export                         |
-| Maximum depth       | Integer | du         | maximum-depth       | blocks above this depth cutoff will be ignored for export                         |
-| No duplications     | Boolean | nd         | no-duplications     | do not export any block that contains at least one strain repeated more than once |
-| Output directory    | String  | o          | output-directory    | path to directory where output will be stored (default: `export`)                 |
-| Prefix              | String  | p          | prefix              | basename of exported files (default: `pangraph`)                                  |
-| GFA                 | Boolean | ng         | no-export-gfa       | toggles whether pangraph is exported as GFA.                                      |
-| PanX                | Boolean | px         | export-panX         | toggles whether pangraph is exported to panX visualization compatible format.     |
+| Name                | Type    | Short Flag | Long Flag           | Description                                                                                         |
+| :------------------ | :------ | :--------- | :------------------ | :-------------------------------------------------------------------------------------------------- |
+| Edge minimum length | Integer | ell        | edge-minimum-length | blocks below this length cutoff will be ignored for edges in graph                                  |
+| Edge maximum length | Integer | elu        | edge-maximum-length | blocks above this length cutoff will be ignored for edges in graph                                  |
+| Edge minimum depth  | Integer | edl        | edge-minimum-depth  | blocks below this depth cutoff will be ignored for edges in graph                                   |
+| Edge maximum depth  | Integer | edu        | edge-maximum-depth  | blocks above this depth cutoff will be ignored for edges in graph                                   |
+| Minimum length      | Integer | ll         | minimum-length      | blocks below this length cutoff will be ignored for export                                          |
+| Maximum length      | Integer | lu         | maximum-length      | blocks above this length cutoff will be ignored for export                                          |
+| Minimum depth       | Integer | dl         | minimum-depth       | blocks below this depth cutoff will be ignored for export                                           |
+| Maximum depth       | Integer | du         | maximum-depth       | blocks above this depth cutoff will be ignored for export                                           |
+| No duplications     | Boolean | nd         | no-duplications     | do not export any block that contains at least one strain repeated more than once                   |
+| Output directory    | String  | o          | output-directory    | path to directory where output will be stored (default: `export`)                                   |
+| Prefix              | String  | p          | prefix              | basename of exported files (default: `pangraph`)                                                    |
+| GFA                 | Boolean | ng         | no-export-gfa       | toggles whether pangraph is exported as GFA.                                                        |
+| PanX                | Boolean | pX         | export-panX         | toggles whether pangraph is exported to panX visualization compatible format. (requires `fasttree`) |
 
 ## Arguments
 Zero or one pangraph file which must be formatted as a JSON.

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -145,6 +145,7 @@ There are a few **optional** external programs that PanGraph can utilize[^1]:
 1. [Mash](https://github.com/marbl/Mash) can be used to construct a guide tree in place of our internal algorithm (see [build](https://neherlab.github.io/pangraph/cli/build/) command options).
 2. [MAFFT](https://mafft.cbrc.jp/alignment/software/) can be optionally used to polish block alignments (see [polish](https://neherlab.github.io/pangraph/cli/polish/) command). Only recommended for short alignments. 
 3. [mmseqs2](https://github.com/soedinglab/MMseqs2) can be used as an alternative alignment kernel to the default *minimap2* (see [build](https://neherlab.github.io/pangraph/cli/build/) command options). It allows merging of more diverged sequences, at the cost of higher computational time.
+4. [fasttree](http://www.microbesonline.org/fasttree/) is used to build phylogenetic trees for export in [PanX](https://github.com/neherlab/pan-genome-analysis)-compatible format (see [export](https://neherlab.github.io/pangraph/cli/export/) command options and the [tutorial section](https://neherlab.github.io/pangraph/tutorials/tutorial_3/#Explore-block-alignments-with-the-panX-visualization)).
 
 In order to invoke all functionalities from PanGraph, these tools must be installed and available on `$PATH`.
 
@@ -153,7 +154,7 @@ It assumes GNU coreutils are available.
 
 These dependencies are already available within the Docker container.
 
-[^1]: We recommend `mmseqs` version `13-45111`, `mash` version `v2.2.2` and `MAFFT` version `v7.475`
+[^1]: We recommend `mmseqs` version `13-45111`, `mash` version `v2.2.2`, `MAFFT` version `v7.475` and `fasttree` version `2.1.11`
 
 ## User's Guide
 

diff --git a/tests/run-cli-tests.sh b/tests/run-cli-tests.sh
@@ -1,14 +1,15 @@
 #!/bin/bash
 set -euxo pipefail
 
-# test that mash, mafft and mmseqs are available in path
+# test that mash, mafft, mmseqs and fasttree are available in path
 echo "mash version:"
 mash --version
 echo "mafft version:"
 mafft --version
 echo "mmseqs version:"
 mmseqs --help | grep "Version"
-
+echo "fasttree help:"
+fasttree -help
 
 # test pangraph commands help
 pangraph help build
@@ -46,9 +47,12 @@ pangraph build -c -k mmseqs -K 8 "$TESTDIR/input.fa" > "$TESTDIR/test3.json"
 echo "Test pangraph polish"
 pangraph polish -c -l 10000 "$TESTDIR/test1.json" > "$TESTDIR/polished.json"
 
-echo "Test pangraph export"
+echo "Test pangraph GFA export"
 pangraph export -o "$TESTDIR/export" "$TESTDIR/test1.json"
 
+echo "Test pangraph PanX export"
+pangraph export -ng -pX -o "$TESTDIR/export" "$TESTDIR/test1.json"
+
 echo "Test pangraph marginalize"
 pangraph marginalize -o "$TESTDIR/marginalize" "$TESTDIR/test1.json"