Add information on iqtree installation

make

@@ -124,11 +124,12 @@ def install_all(install_dir, target, dev=False, user=False):
             msg += ("\t- mafft (to align persistent genomes in order to infer a phylogenetic tree "
                     "after)\n")
         if "trees" in to_install_user:
-            msg += ("\t- One of the 3 following softwares, used to infer a phylogenetic tree:\n"
+            msg += ("\t- One of the 4 following softwares, used to infer a phylogenetic tree:\n"
                     "\t\t* FastTree (see README or documentation for more information on how to "
                     "install it)\n"
                     "\t\t* FastME\n"
-                    "\t\t* Quicktree\n")
+                    "\t\t* Quicktree\n"
+                    "\t\t* IQtree (or IQtree2)")
         msg += ("See more information on how to download/install those softwares in README or in "
                 "documentation.")
         logger.warning(msg)
@@ -160,7 +161,7 @@ def check_dependencies(target):
         if not cmd_exists("mafft"):
             to_install_user.append("mafft")
         if not cmd_exists("FastTreeMP") and not cmd_exists("fastme") and not cmd_exists(
-                "quicktree"):
+                "quicktree") and not cmd_exists("iqtree") and not cmd_exists("iqtree2"):
             to_install_user.append("trees")
     return to_install_user
 

test/test_install/test_make_all-installed.py

@@ -145,6 +145,7 @@ def test_uninstall(install_panacota):
     assert utils.check_installed("prokka")
     assert utils.check_installed("mash")
     assert utils.check_installed("quicktree")
+    assert utils.check_installed("iqtree") or utils.check_installed("iqtree2")
     logfile = "install.log"
     with open(logfile, "r") as logf:
         lines = logf.readlines()

test/test_install/test_make_barrnap.py

@@ -71,9 +71,9 @@ def test_install():
                "- prokka (for annotate subcommand, with syntaxic + functional annotation)",
                "- prodigal : for annotate subcommand, you at least need prodigal (for syntaxic "
                "annotation only). If you even need functional annotation, also install prokka",
-               "- One of the 3 following softwares, used to infer a phylogenetic tree:",
+               "- One of the 4 following softwares, used to infer a phylogenetic tree:",
                "* FastTree (see README or documentation for more information on how to "
-               "install it)", "* FastME", "* Quicktree"]
+               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)"]
     # Check output logfile content. Check that all content is present, in any order.
     with open(logfile, "r") as logf:
         logf_content = "".join(logf.readlines())
@@ -165,9 +165,9 @@ def test_develop():
                "- prokka (for annotate subcommand, with syntaxic + functional annotation). "
                "If you only need syntaxic annotation, prodigal is enough.",
                "- prodigal : for annotate subcommand, you at least need prodigal (for syntaxic ",
-               "- One of the 3 following softwares, used to infer a phylogenetic tree:",
+               "- One of the 4 following softwares, used to infer a phylogenetic tree:",
                "* FastTree (see README or documentation for more information on how to "
-               "install it)", "* FastME", "* Quicktree", "DONE"]
+               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)", "DONE"]
     # Check output logfile content. Check that all content is present, in any order.
     with open(logfile, "r") as logf:
         logf_content = "".join(logf.readlines())

test/test_install/test_make_prodigal.py

@@ -76,9 +76,9 @@ def test_install_panacota():
                "- prokka (for annotate subcommand, with syntaxic + functional annotation). "
                "If you only need syntaxic annotation, prodigal is enough.",
                "- barrnap. If you use Prokka for functional annotation, it will not predict RNA.",
-               "- One of the 3 following softwares, used to infer a phylogenetic tree:",
+               "- One of the 4 following softwares, used to infer a phylogenetic tree:",
                "* FastTree (see README or documentation for more information on how to "
-               "install it)", "* FastME", "* Quicktree"]
+               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)"]
     # Check output logfile content. Check that all content is present, in any order.
     with open(logfile, "r") as logf:
         logf_content = "".join(logf.readlines())
@@ -176,9 +176,9 @@ def test_develop():
                "after)",
                "- prokka (for annotate subcommand, with syntaxic + functional annotation). "
                "If you only need syntaxic annotation, prodigal is enough.",
-               "- One of the 3 following softwares, used to infer a phylogenetic tree:",
+               "- One of the 4 following softwares, used to infer a phylogenetic tree:",
                "* FastTree (see README or documentation for more information on how to "
-               "install it)", "* FastME", "* Quicktree", "DONE"]
+               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)", "DONE"]
     # Check output logfile content. Check that all content is present, in any order.
     with open(logfile, "r") as logf:
         logf_content = "".join(logf.readlines())
@@ -224,9 +224,9 @@ def test_install_user():
                "after)",
                "- prokka (for annotate subcommand, with syntaxic + functional annotation). "
                "If you only need syntaxic annotation, prodigal is enough.",
-               "- One of the 3 following softwares, used to infer a phylogenetic tree:",
+               "- One of the 4 following softwares, used to infer a phylogenetic tree:",
                "* FastTree (see README or documentation for more information on how to "
-               "install it)", "* FastME", "* Quicktree", "DONE"]
+               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)", "DONE"]
     with open(logfile, "r") as logf:
         logf_content = "".join(logf.readlines())
         for linec in content:

test/test_install/test_make_prokka-quicktree.py

@@ -38,6 +38,7 @@ def test_install_prokka_quicktree():
     assert not utils.check_installed("barrnap")
     assert not utils.check_installed("prodigal")
     assert utils.check_installed("quicktree")
+    assert not utils.check_installed("iqtree")
     assert utils.check_installed("prokka")
     assert not utils.check_installed("PanACoTA")
     assert utils.check_installed('quicktree')

test/test_install/test_make_ubuntu.py

@@ -36,6 +36,8 @@ def test_install_panacota_base_ubuntu():
     assert not utils.check_installed("quicktree")
     assert not utils.check_installed("fastme")
     assert not utils.check_installed("FastTreeMP")
+    assert not utils.check_installed("iqtree")
+    assert not utils.check_installed("iqtree2")
     assert not utils.check_installed("mash")
     utils.run_cmd(cmd, error)
     assert not utils.check_installed("barrnap")
@@ -46,6 +48,8 @@ def test_install_panacota_base_ubuntu():
     assert not utils.check_installed("quicktree")
     assert not utils.check_installed("fastme")
     assert not utils.check_installed("FastTreeMP")
+    assert not utils.check_installed("iqtree")
+    assert not utils.check_installed("iqtree2")
     assert not utils.check_installed("mash")
     assert utils.check_installed("PanACoTA")
     cmd = "pip3 show PanACoTA"
@@ -75,10 +79,10 @@ def test_install_panacota_base_ubuntu():
                "- prokka (for annotate subcommand, with syntaxic + functional annotation). "
                "If you only need syntaxic annotation, prodigal is enough.",
                "- barrnap. If you use Prokka for functional annotation, it will not predict RNA.",
-               "- mmseqs (for pangenome subcommand)",  "* Quicktree",
+               "- mmseqs (for pangenome subcommand)",  "* Quicktree", "* IQtree (or IQtree2)",
                "- mafft (to align persistent genomes in order to infer a phylogenetic "
                "tree after)",
-               "- One of the 3 following softwares, used to infer a phylogenetic tree:",
+               "- One of the 4 following softwares, used to infer a phylogenetic tree:",
                "* FastTree (see README or documentation for more information on how to "
                "install it)", "* FastME", "See more information on how to "
                "download/install those softwares in README or in documentation."]
@@ -140,9 +144,9 @@ def test_develop():
                "- prokka (for annotate subcommand, with syntaxic + functional annotation). "
                "If you only need syntaxic annotation, prodigal is enough.",
                "- prodigal : for annotate subcommand, you at least need prodigal (for syntaxic ",
-               "- One of the 3 following softwares, used to infer a phylogenetic tree:",
+               "- One of the 4 following softwares, used to infer a phylogenetic tree:",
                "* FastTree (see README or documentation for more information on how to "
-               "install it)", "* FastME", "* Quicktree"]
+               "install it)", "* FastME", "* Quicktree", "* IQtree (or IQtree2)"]
     # Check output logfile content. Check that all content is present, in any order.
     with open(logfile, "r") as logf:
         logf_content = "".join(logf.readlines())