training_dataset.config: update conda path to use .conda_envs link

src/training_dataset.config

@@ -119,7 +119,7 @@ profiles {
     process{
       withName: build_synthetic_bed {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/bedtools_2.25.0"
+        conda = "src/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
@@ -129,7 +129,7 @@ profiles {
       }
       withName: fasta_from_bed {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/bedtools_2.25.0"
+        conda = "src/.conda_envs/bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1
@@ -139,7 +139,7 @@ profiles {
       }
       withName: index_fasta {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/bowtie2_2.3.4.1"
+        conda = "src/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -150,7 +150,7 @@ profiles {
       }
       withName: mapping_fastq_paired {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/bowtie2_2.3.4.1"
+        conda = "src/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -161,7 +161,7 @@ profiles {
       }
       withName: bam_2_fastq_paired {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/samtools_1.7"
+        conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -172,7 +172,7 @@ profiles {
       }
       withName: sort_bam_paired {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/samtools_1.7"
+        conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -183,7 +183,7 @@ profiles {
       }
       withName: index_bam_paired {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/samtools_1.7"
+        conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -194,7 +194,7 @@ profiles {
       }
       withName: mapping_fastq_single {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/bowtie2_2.3.4.1"
+        conda = "src/.conda_envs/bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -205,7 +205,7 @@ profiles {
       }
       withName: bam_2_fastq_single {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/samtools_1.7"
+        conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -216,7 +216,7 @@ profiles {
       }
       withName: sort_bam_single {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/samtools_1.7"
+        conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16
@@ -227,7 +227,7 @@ profiles {
       }
       withName: index_bam_single {
         beforeScript = "./src/conda_psmn.sh"
-        conda = "$CONDA_ENVS/samtools_1.7"
+        conda = "src/.conda_envs/samtools_1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16