diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 61d44aef2be3abfb942a97dd22fc599574ff7a31..78a2b161680ddaf01c1bb349c658b7afcd6e2b9f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -52,6 +52,24 @@ sphinx-documentation:
# Run sphinx-build (treating warnings as errors)
sphinx-build -W docs/source output
+conda-test:
+ stage: test
+ script:
+ - |
+ # Install system dependencies
+ apt-get install --yes --no-install-recommends git bzip2
+
+ # Install micromamba
+ curl -Ls https://micromamba.snakepit.net/api/micromamba/linux-64/1.4.2 | tar xvj bin/micromamba
+ chmod +x ./bin/micromamba
+ export MAMBA_ROOT_PREFIX=/opt/micromamba
+ ./bin/micromamba shell --yes init ${MAMBA_ROOT_PREFIX}
+ source /root/.bashrc
+
+ # Test creation conda environment
+ micromamba env create --dry-run --name pantools --yes --strict-channel-priority \
+ --channel conda-forge --channel bioconda --file conda.yaml
+
unit-tests:
stage: test
script:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6bf3f50232dedfee51dca4cc5c4855fdc39df909..922a84ed94a2980f4c2d49272866ed82d2b50f58 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -3,12 +3,19 @@ repos:
hooks:
- id: pre-commit-validate-config
name: Validate pre-commit config
- description: 'Validates the .pre-commit-config.yaml file'
+ description: 'Validates the .pre-commit-config.yaml file.'
files: '.pre-commit-config.yaml'
entry: pre-commit-validate-config
args:
- .pre-commit-config.yaml
language: system
+ - id: conda-yaml-validate
+ name: Validate conda YAML
+ description: 'Validates conda.yaml for creation of conda environment.'
+ files: 'conda.yaml'
+ entry: mamba
+ args: [env, create, -d, -n=test_pantools, -f=conda.yaml]
+ language: system
- id: maven-compile
name: Compile with Maven
description: 'Compile all code with mvn compile.'
diff --git a/CHANGELOG.md b/CHANGELOG.md
index d9f3ff4eebe8bb2b32c732fa4f7f8ea0bbb7a223..75f1ca8e51baee1103e93b9a44159e5393991ac1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,8 @@ All notable changes to Pantools will be documented in this file.
### Changed
- `pantools busco_protein`, `pantools gene_classification`, `pantools kmer_classification`, `pantools group_info`, `pantools rename_phylogeny`, `pantools create_tree_template`, `pantools core_phylogeny`, `pantools rename_matrix` to be compatible with possible added phasing information in a pangenome database (!148).
- `busco_protein` is no longer functional with BUSCO v3 and odb9 datasets (!146).
+- `conda_linux.yaml` and `conda_macos.yaml` now unified in one `conda.yaml` file (!203).
+- Updated KMC version to >=3.1.0 (!203).
### Fixed
- `pantools core_phylogeny` and `pantools consensus_tree` now ignore MSAs that could not be trimmed (!197).
diff --git a/README.md b/README.md
index 787780a78aa19ca38271e3b5315e26b5372d295c..d77b489a53e7d7ed48fb8100ccd4ea77873021f7 100755
--- a/README.md
+++ b/README.md
@@ -50,8 +50,7 @@ git checkout v4.0.0
We provide conda environments for installing all dependencies of PanTools, which can be installed using conda/mamba (we recommend using mamba):
```bash
-mamba env create -n pantools -f conda_linux.yaml # for linux
-mamba env create -n pantools -f conda_macos.yaml # for macOS (does not include busco)
+mamba env create -n pantools -f conda.yaml
```
## Building a runnable jar
diff --git a/conda_linux.yaml b/conda.yaml
similarity index 88%
rename from conda_linux.yaml
rename to conda.yaml
index 8da2a955552c26419019b4dea77f16eddea8c13f..4e05083448468104a08392a1a8a40b2a48d689b7 100644
--- a/conda_linux.yaml
+++ b/conda.yaml
@@ -4,8 +4,7 @@ channels:
dependencies:
- openjdk=8.0
- maven
- - python=3.7
- - kmc=3.0.1
+ - kmc>=3.1.0
- mcl
- mafft
- iqtree
@@ -13,7 +12,7 @@ dependencies:
- mash=2.3
- fastani
- busco=5
- - r-base
+ - r-base>=3.5
- r-ggplot2
- r-ape
- graphviz
diff --git a/conda_macos.yaml b/conda_macos.yaml
deleted file mode 100644
index 6225cc6c281867e19859e2abb192ca23a03039bf..0000000000000000000000000000000000000000
--- a/conda_macos.yaml
+++ /dev/null
@@ -1,26 +0,0 @@
-channels:
- - conda-forge
- - bioconda
-dependencies:
- - openjdk=8.0
- - maven
- - python=3.7
- - kmc=3.0.1
- - mcl
- - mafft
- - iqtree
- - fasttree
- - mash=2.3
- - fastani
- #- busco=5 #causes conflicts
- - r-base
- - r-ggplot2
- - r-ape
- - graphviz
- - aster=1.3
- #- bcftools>=1.12 #can only be installed from this YAML without strict channel priority
- - tabix
- - blast
- - pal2nal>=14.1
- - paml>=4.10.6
- #- r-cowplot>=1.1.1 #causes conflicts
diff --git a/docs/source/developer_guide/install.rst b/docs/source/developer_guide/install.rst
index 2025d2a1b9994cf8fce8fb478c968b81857e120f..dc22dbef581c614105281141a1a475474bf331f8 100644
--- a/docs/source/developer_guide/install.rst
+++ b/docs/source/developer_guide/install.rst
@@ -27,19 +27,16 @@ below.
Install dependencies using Conda
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-To install all dependencies into a separate environment, run the
-following commands. Please choose the conda_linux.yaml or
-conda_macos.yaml file depending on your operating system. These files
-be found in the `release <https://git.wur.nl/bioinformatics/pantools/-/
-releases>`_ or in the PanTools home when working with the git itself. There is a
-difference between the two files because not all tools are available for macOS.
-For smooth dependency resolving with conda, it is recommended to use strict
-channel priority and to only use the bioconda and conda-forge channels.
+To install all dependencies into a separate environment, run the following
+commands. Please use the conda.yaml file which can be found in the
+`release <https://git.wur.nl/bioinformatics/pantools/-/releases>`_ or in the
+PanTools home when working with the git itself. For smooth dependency resolving
+with conda, it is recommended to use strict channel priority and to only use the
+bioconda and conda-forge channels.
.. code:: bash
- $ mamba env create -n pantools -f conda_linux.yaml #for Linux
- $ mamba env create -n pantools -f conda_macos.yaml #for macOS
+ $ mamba env create -n pantools -f conda.yaml
--------------
diff --git a/docs/source/developer_guide/release.rst b/docs/source/developer_guide/release.rst
index f5875ce5a8053b9469bc2c5097ed32d904cfbd31..dccaf5d4cc02ea71f92d5f0eab5a5b52a262fcdc 100644
--- a/docs/source/developer_guide/release.rst
+++ b/docs/source/developer_guide/release.rst
@@ -16,6 +16,6 @@ The following steps are required to create a new release of PanTools:
and delete the **new release branch**.
9. Put a tag on the merge commit in the **current stable release branch**.
10. Locally compile PanTools and put the compiled JAR file on the server.
-11. Create a release from the tag and attach 1) the compiled JAR file, 2) the
- ``conda_linux.yaml`` file, and 3) the ``conda_macos.yaml`` file.
+11. Create a release from the tag and attach 1) the compiled JAR file, and 2)
+ the ``conda.yaml`` file.
12. Update the bioconda recipe for the new release.
diff --git a/docs/source/user_guide/install.rst b/docs/source/user_guide/install.rst
index c88de86ec8128077646e5230dbdce22741ed2a78..0a7f37345b44057884f6af8284c83b6ed6e40b59 100644
--- a/docs/source/user_guide/install.rst
+++ b/docs/source/user_guide/install.rst
@@ -20,8 +20,8 @@ For users that don't have conda installed, we recommend to install conda first:
.. substitution-code-block:: bash
- $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
- $ bash Miniconda3-latest-Linux-x86_64.sh
+ $ curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+ $ bash Miniforge3-$(uname)-$(uname -m).sh
# Follow the instructions on the screen
# Restart your terminal
@@ -34,23 +34,13 @@ For users that don't have conda installed, we recommend to install conda first:
# Restart your terminal
-Next, we recommend to install mamba into the conda base environment to enable
-much faster dependency solving:
-
-.. substitution-code-block:: bash
-
- $ conda install -n base mamba
-
-Finally, we can install PanTools. We recommend to install PanTools into a
+Now, we can install PanTools. We recommend to install PanTools into a
separate environment. Please make sure you install the most recent versions of
the tools.
-NB: not all dependencies are available for macOS, therefore please use the
-correct line from this code block depending on your operating system:
.. substitution-code-block:: bash
- $ mamba create -n pantools pantools bcftools busco # Linux
- $ mamba create -n pantools pantools # macOS
+ $ mamba create -n pantools pantools
Please make sure to activate the environment before using PanTools:
@@ -77,19 +67,15 @@ environment that has all dependencies.
Install dependencies using conda
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Please choose the conda_linux.yaml or conda_macos.yaml file depending on your
-operating system. These files be found on the
-`release page <https://git.wur.nl/bioinformatics/pantools/-/releases>`_. The
-difference between the two files comes from some dependencies conflicting on
-macOS but not on Linux. Only on Linux a full installation of PanTools is
-possible. On macOS, some functionalities will not be available.
+All dependencies are listed in conda.yaml which can be found on the
+`release page <https://git.wur.nl/bioinformatics/pantools/-/releases>`_.
For users that don't have conda installed, we recommend to install conda first:
.. substitution-code-block:: bash
- $ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
- $ bash Miniconda3-latest-Linux-x86_64.sh
+ $ curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
+ $ bash Miniforge3-$(uname)-$(uname -m).sh
# Follow the instructions on the screen
# Restart your terminal
@@ -102,19 +88,11 @@ For users that don't have conda installed, we recommend to install conda first:
# Restart your terminal
-Next, we recommend to install mamba into the conda base environment to enable
-much faster dependency solving:
-
-.. substitution-code-block:: bash
-
- $ conda install mamba -n base -c conda-forge
-
-Finally, we can install all dependencies into a separate environment:
+Now, we can install all dependencies into a separate environment:
.. substitution-code-block:: bash
- $ mamba env create -n pantools -f conda_linux.yaml #for Linux
- $ mamba env create -n pantools -f conda_macos.yaml #for macOS
+ $ mamba env create -n pantools -f conda.yaml
Please make sure to activate the environment before using PanTools:
diff --git a/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java b/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java
index b92287659e08f111b4d766a026a7d28d30e26338..4043a4fad2969e06818ec0f3222976762da8a177 100755
--- a/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java
+++ b/src/main/java/nl/wur/bif/pantools/construction/index/IndexDatabase.java
@@ -16,7 +16,7 @@ import java.util.logging.Level;
import java.util.logging.Logger;
import static nl.wur.bif.pantools.utils.Globals.*;
-import static nl.wur.bif.pantools.utils.Utils.executeCommand;
+import static nl.wur.bif.pantools.utils.Utils.runCommandWithOutput;
/**
* Implements all the functionality to build a KMC-based kmer index.
@@ -179,7 +179,7 @@ public final class IndexDatabase {
public IndexDatabase(String index_path, String genomes_path_file, SequenceDatabase genomeDb, int k) {
int i, j, number_of_pages, record_size, page_size, full_page_size;
long number_of_prefixes, longest_scaffold = 0;
- Pantools.logger.info("Creating index in {}", index_path);
+ Pantools.logger.debug("Creating index in {}", index_path);
try {
Files.createDirectory(Paths.get(index_path));
Run_KMC(index_path, genomes_path_file, genomeDb, k);
@@ -212,7 +212,7 @@ public final class IndexDatabase {
offset_len = (int)Math.round(Math.ceil( Math.log(longest_scaffold) / Math.log(2) / 8));
poniter_length = 2 * id_len + offset_len + 1;
write_info(index_path, "sorted");
- Pantools.logger.info("Indexing kmers...");
+ Pantools.logger.debug("Indexing kmers...");
// load the prefix file into the memory
Pantools.logger.trace("Loading prefixes in memory...");
number_of_prefixes = 1 << (2 * pre_len);
@@ -283,21 +283,31 @@ public final class IndexDatabase {
// move current index files to directory old_darabase
try{
- // make new index for new genomes
+ // make new index for new genomes
Pantools.logger.info("Running KMC with K = {} ...", old_database.K);
- executeCommand(KMC + " -cs127 -r -k" + old_database.K + " -t" + THREADS + " -ci1 -fm " + (genomeDb.num_genomes - previous_num_genomes > 1 ? "@" +
+ final String index_command = KMC + " -cs127 -r -k" + old_database.K + " -t" + THREADS + " -ci1 -fm " + (genomeDb.num_genomes - previous_num_genomes > 1 ? "@" +
genomes_path_file.trim() : genomeDb.genome_names[previous_num_genomes + 1]) +
- " " + index_path + "new " + index_path);
-
-
-
- // merge two indeces
- executeCommand(KMC + "_tools union " + index_path + "sorted " + index_path + "new " + index_path + "merged");
+ " " + index_path + "new " + index_path;
+ Pantools.logger.debug("KMC command: {}", index_command);
+
+ final String index_output = runCommandWithOutput(index_command);
+ Pantools.logger.trace("KMC output: {}", index_output);
+
+ // merge two indices
+ Pantools.logger.debug("Merging two indices.");
+
+ final String merge_command = KMC + "_tools simple union " + index_path + "sorted " + index_path + "new " + index_path + "merged";
+ Pantools.logger.debug("KMC command: {}", merge_command);
+
+ final String merge_output = runCommandWithOutput(merge_command);
+ Pantools.logger.trace("KMC output: {}", merge_output);
+
pre_file = new RandomAccessFile(index_path + "merged" + PREFIX_FILE_EXTENTION, "r");
pre_file.seek(pre_file.length() - 8);
header_pos = read_int(pre_file);
pre_file.seek(pre_file.length() - 8 - header_pos);
- // read the merged index properties
+
+ // read the merged index properties
K = read_int(pre_file);
mode = read_int(pre_file);
ctr_size = read_int(pre_file);
@@ -314,10 +324,11 @@ public final class IndexDatabase {
offset_len = (int)Math.round(Math.ceil( Math.log(longest_scaffold) / Math.log(2) / 8));
poniter_length = 2 * id_len + offset_len + 1;
write_info(index_path, "merged");
- Pantools.logger.info("number of available kmers:\t{}", old_database.kmers_num);
- Pantools.logger.info("number of new kmers:\t{}", (kmers_num - old_database.kmers_num));
+ Pantools.logger.info("Number of available kmers:\t{}", old_database.kmers_num);
+ Pantools.logger.info("Number of new kmers:\t{}", (kmers_num - old_database.kmers_num));
Pantools.logger.info("Total number of kmers:\t{}", kmers_num);
- // load the prefix file into the memory
+
+ // load the prefix file into the memory
Pantools.logger.trace("loading new prefixes in memory...");
number_of_prefixes = 1 << (2 * pre_len);
prefix_ptr = new long[(int)number_of_prefixes];
@@ -335,7 +346,8 @@ public final class IndexDatabase {
}
pre_buff = null;
pre_file.close();
- // mapping suffix file into the memory
+
+ // mapping suffix file into the memory
Pantools.logger.trace("Mapping new suffix file to memory...");
record_size = ctr_size + suf_len / 4;
full_page_size = MAX_BYTE_COUNT / record_size * record_size; // in bytes
@@ -422,60 +434,46 @@ public final class IndexDatabase {
*/
public void Run_KMC(String index_path, String genomes_path_file, SequenceDatabase genomeDb, int k) {
double p = 0;
- String output;
try{
Runtime.getRuntime().exec(KMC); // to check if kmc is reachable
if (k > -1) { // K is not given by the user, then calculate the optimal K
+ Pantools.logger.info("K is given by the user: {}", k);
+
K = k;
if (K % 2 == 0) // Even values are problamatic to localization process
K += 1;
-
- String kmc_command = KMC + " -cs127 -k" + K + " -t" + THREADS + " -ci1 -fm " +
+
+ final String kmc_command = KMC + " -cs127 -k" + K + " -t" + THREADS + " -ci1 -fm " +
(genomeDb.num_genomes > 1 ? "@" + genomes_path_file.trim() : genomeDb.genome_names[1]) + " " + index_path + "/kmers " + index_path;
Pantools.logger.debug("KMC command: {}", kmc_command);
- executeCommand(kmc_command);
- if (new File(index_path + "/kmers.kmc_pre").exists() && new File(index_path + "/kmers.kmc_suf").exists()) {
- final String kmcSortCommand = String.format(
- "kmc_tools -t%1$d sort %2$s/kmers %2$s/sorted",
- THREADS,
- index_path);
- output = executeCommand(kmcSortCommand);
- // Small databases are usually sorted already
- if (output.startsWith("This database contains sorted k-mers already!")) {
- new File(index_path + "/kmers.kmc_pre").renameTo(new File(index_path + "/sorted.kmc_pre"));
- new File(index_path + "/kmers.kmc_suf").renameTo(new File(index_path + "/sorted.kmc_suf"));
- } else {
- new File(index_path + "/kmers.kmc_pre").delete();
- new File(index_path + "/kmers.kmc_suf").delete();
- }
+ final String output = runCommandWithOutput(kmc_command);
+ Pantools.logger.trace("KMC output: {}", output);
+
+ if (checkIfKmcIndexExists(index_path)) {
+ sortKmcIndex(index_path);
} else {
Pantools.logger.error("No kmc index found in {}", index_path);
- System.exit(1);
+ throw new RuntimeException("Missing kmc index");
}
} else {
+ Pantools.logger.info("K is not given by the user. Calculating the optimal K.");
+
K = Math.round((float)(Math.log(genomeDb.number_of_bytes * 200)/Math.log(4)));
K += (K % 2 == 0 ? 1 : 0);
do {
K -= 2;
- Pantools.logger.info("K = {}", K);
- String kmc_command = KMC + " -cs127 -k" + K + " -t" + THREADS + " -ci1 -fm " +
+ Pantools.logger.debug("K = {}", K);
+
+ final String kmc_command = KMC + " -cs127 -k" + K + " -t" + THREADS + " -ci1 -fm " +
(genomeDb.num_genomes > 1 ? "@" + genomes_path_file.trim() : genomeDb.genome_names[1]) + " " + index_path + "/kmers " + index_path;
Pantools.logger.debug("KMC command: {}", kmc_command);
- executeCommand(kmc_command);
- if (new File(index_path + "/kmers.kmc_pre").exists() && new File(index_path + "/kmers.kmc_suf").exists()) {
- final String kmcSortCommand = String.format(
- "kmc_tools -t%1$d sort %2$s/kmers %2$s/sorted",
- THREADS,
- index_path);
- output = executeCommand(kmcSortCommand);
- // Small databases are usually sorted already
- if (output.startsWith("This database contains sorted k-mers already!")) {
- new File(index_path + "/kmers.kmc_pre").renameTo(new File(index_path + "/sorted.kmc_pre"));
- new File(index_path + "/kmers.kmc_suf").renameTo(new File(index_path + "/sorted.kmc_suf"));
- } else {
- new File(index_path + "/kmers.kmc_pre").delete();
- new File(index_path + "/kmers.kmc_suf").delete();
- }
+
+ final String kmc_output = runCommandWithOutput(kmc_command);
+ Pantools.logger.trace("KMC output: {}", kmc_output);
+
+ if (checkIfKmcIndexExists(index_path)) {
+ sortKmcIndex(index_path);
+
pre_file = new RandomAccessFile(index_path + "/sorted.kmc_pre", "r");
pre_file.seek(pre_file.length() - 8);
header_pos = read_int(pre_file);
@@ -499,37 +497,66 @@ public final class IndexDatabase {
pre_file.close();
} else {
Pantools.logger.error("No kmc index found in {}", index_path);
- System.exit(1);
+ throw new RuntimeException("Missing kmc index");
}
} while (p < 0.01);
K += 2;
- executeCommand(KMC + " -cs127 -k" + K + " -t" + THREADS + " -ci1 -fm " +
- (genomeDb.num_genomes > 1 ? "@" + genomes_path_file.trim() : genomeDb.genome_names[1]) + " " + index_path + "/kmers " + index_path);
- if (new File(index_path + "/kmers.kmc_pre").exists() && new File(index_path + "/kmers.kmc_suf").exists()) {
- final String kmcSortCommand = String.format(
- "kmc_tools -t%1$d sort %2$s/kmers %2$s/sorted",
- THREADS,
- index_path);
- output = executeCommand(kmcSortCommand);
- // Small databases are usually sorted already
- if (output.startsWith("This database contains sorted k-mers already!")) {
- new File(index_path + "/kmers.kmc_pre").renameTo(new File(index_path + "/sorted.kmc_pre"));
- new File(index_path + "/kmers.kmc_suf").renameTo(new File(index_path + "/sorted.kmc_suf"));
- } else {
- new File(index_path + "/kmers.kmc_pre").delete();
- new File(index_path + "/kmers.kmc_suf").delete();
- }
+
+ final String kmc_command = KMC + " -cs127 -k" + K + " -t" + THREADS + " -ci1 -fm " +
+ (genomeDb.num_genomes > 1 ? "@" + genomes_path_file.trim() : genomeDb.genome_names[1]) + " " + index_path + "/kmers " + index_path;
+ Pantools.logger.debug("KMC command: {}", kmc_command);
+
+ final String kmc_output = runCommandWithOutput(kmc_command);
+ Pantools.logger.trace("KMC output: {}", kmc_output);
+
+ if (checkIfKmcIndexExists(index_path)) {
+ sortKmcIndex(index_path);
} else {
Pantools.logger.error("No kmc index found in {}", index_path);
- System.exit(1);
+ throw new RuntimeException("Missing kmc index");
}
}
- Pantools.logger.info("K = {}", K);
+ Pantools.logger.debug("K = {}", K);
} catch (IOException ex) {
Pantools.logger.warn("Failed to find K!");
}
}
+ /**
+ * Checks if the KMC index exists in the given path
+ * @param index_path Path to the index database
+ * @return True if the KMC index exists, false otherwise
+ */
+ private boolean checkIfKmcIndexExists(String index_path) {
+ Pantools.logger.debug("Checking if kmc index exists in {}", index_path);
+ boolean indexExists = new File(index_path + "/kmers.kmc_pre").exists() && new File(index_path + "/kmers.kmc_suf").exists();
+ Pantools.logger.trace("KMC index exists: {}", indexExists);
+ return indexExists;
+ }
+
+ /**
+ * Sorts the KMC index in the given path
+ * @param index_path Path to the index database
+ */
+ private void sortKmcIndex(String index_path) {
+ Pantools.logger.debug("Sorting kmc index in {}", index_path);
+
+ final String command = KMC + "_tools transform " + index_path + "/kmers sort " + index_path + "/sorted";
+ Pantools.logger.debug("KMC command: {}", command);
+
+ final String output = runCommandWithOutput(command);
+ Pantools.logger.trace("KMC output: {}", output);
+
+ // Small databases are usually sorted already
+ if (output.startsWith("Warning: input database is already sorted.")) {
+ new File(index_path + "/kmers.kmc_pre").renameTo(new File(index_path + "/sorted.kmc_pre"));
+ new File(index_path + "/kmers.kmc_suf").renameTo(new File(index_path + "/sorted.kmc_suf"));
+ } else {
+ new File(index_path + "/kmers.kmc_pre").delete();
+ new File(index_path + "/kmers.kmc_suf").delete();
+ }
+ }
+
/**
* Writes the index database specification in the info file of the index database
*
diff --git a/src/main/java/nl/wur/bif/pantools/utils/Utils.java b/src/main/java/nl/wur/bif/pantools/utils/Utils.java
index 502569e8b70dbe621c98a9d39ed7be1937297844..aab4ca5681677b19f743799893b628a3d530a56e 100644
--- a/src/main/java/nl/wur/bif/pantools/utils/Utils.java
+++ b/src/main/java/nl/wur/bif/pantools/utils/Utils.java
@@ -540,25 +540,29 @@ public final class Utils {
/**
* Executes a shell command.
- *
- * @param command The command
- * @return The output of the bash command
- */
- public static String executeCommand(String command) {
- StringBuilder exe_output = new StringBuilder();
- String line = "";
- Process p;
+ * @param command the shell command
+ * @return the output (both stdout and stderr) of the command
+ */
+ public static String runCommandWithOutput(String command) {
+ List<String> cmd = new ArrayList<>();
+ cmd.add("sh");
+ cmd.add("-c");
+ cmd.add(command);
+ ProcessBuilder pb = new ProcessBuilder(cmd);
try {
- p = Runtime.getRuntime().exec(command);
+ Process p = pb.start();
p.waitFor();
BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
+ StringBuilder output = new StringBuilder();
+ String line;
while ((line = reader.readLine()) != null) {
- exe_output.append(line).append("\n");
+ output.append(line).append("\n");
}
- } catch (Exception e) {
+ return output.toString();
+ } catch (IOException | InterruptedException e) {
e.printStackTrace();
+ throw new RuntimeException(e.getMessage());
}
- return exe_output.toString();
}
/**