diff --git a/pipeline/Makefile b/pipeline/Makefile
index 894183e71..5d1b02316 100644
--- a/pipeline/Makefile
+++ b/pipeline/Makefile
@@ -1,48 +1,35 @@
 # set the working directory where the makefile will be created and analysis will be done.
 
-WORKDIR=./test
+TEMP_DIR = ~/tmp
 
 # analysis-specific files.
 
-SPEC=templates/metabarcode_qc/metabarcode_spec.hjson
-TEMPLATE=templates/metabarcode_qc/metabarcode_makefile.html
+SPEC=templates/qc/qc_spec.hjson
+TEMPLATE=templates/qc/qc_makefile.html
 COMMAND=all
 
-# check if spec file exists.
+TEST_DATA=$(TEMP_DIR)/data.tar.gz
+SAMPLE_DATA=$(TEMP_DIR)/sampleinfo.txt
 
-ifeq ($(wildcard $(SPEC)),)
-$(error $(SPEC) not found.)
-endif
-
-# check if template file exists.
-
-ifeq ($(wildcard $(TEMPLATE)),)
-$(error $(TEMPLATE) not found.)
-endif
+run: setup
+	@echo runs all commands to setup the pipeline and then runs it.
 
+$(TEMP_DIR):
+	mkdir -p $(TEMP_DIR)
 
-workdir:
-	#
-	# creates work directory.
-	#
-	mkdir -p $(WORKDIR)
+$(TEST_DATA): $(TEMP_DIR)
+	curl -o $(TEST_DATA) -O http://iris.bx.psu.edu/projects/metabarcode-data/data.tar.gz
 
-get_data: workdir
-	#
-	# Download data and sampleinfo to workdir.
-	#
-	wget -P $(WORKDIR) http://iris.bx.psu.edu/projects/metabarcode-data/data.tar.gz
-	wget -P $(WORKDIR) http://iris.bx.psu.edu/projects/metabarcode-data/sampleinfo.txt
+$(SAMPLE_DATA): $(TEMP_DIR)
+	 curl -o $(SAMPLE_DATA) -O http://iris.bx.psu.edu/projects/metabarcode-data/sampleinfo.txt
 
-setup:
+setup: $(TEST_DATA) $(SAMPLE_DATA)
 	#
 	# creates the makefile and runs the pipeline.
 	#
-	python make.py $(SPEC) $(TEMPLATE) > $(WORKDIR)/Makefile
+	#python make.py $(SPEC) $(TEMPLATE) > $(WORKDIR)/Makefile
 	#
 	# runs make
 	#
-	cd $(WORKDIR); make $(COMMAND)
+	#cd $(WORKDIR); make $(COMMAND)
 
-run: workdir get_data setup
-	@echo runs all commands to setup the pipeline and then runs it.
diff --git a/pipeline/classify/__init__.py b/pipeline/classify/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/pipeline/classify/test.py b/pipeline/classify/test.py
new file mode 100644
index 000000000..02aca1c9f
--- /dev/null
+++ b/pipeline/classify/test.py
@@ -0,0 +1 @@
+print("HELLO")
diff --git a/pipeline/data/__init__.py b/pipeline/data/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/pipeline/samplesheet.py b/pipeline/data/samplesheet.py
similarity index 96%
rename from pipeline/samplesheet.py
rename to pipeline/data/samplesheet.py
index c0193352c..234bd94bd 100644
--- a/pipeline/samplesheet.py
+++ b/pipeline/data/samplesheet.py
@@ -69,14 +69,14 @@ def get_fnames(sname , datadir):
 if __name__ == "__main__":
 
     samplesheet = sys.argv[1]
-    datadir =sys.argv[2]
+    datadir = sys.argv[2]
 
     #samplesheet ="./test/sampleinfo.txt"
     #datadir ="test/data"
 
     data = update_sampleinfo(samplesheet, datadir)
 
-    outfile = open("updated_sampleinfo.txt", "w")
+    outfile = sys.stdout
     header ="\t".join(['sample_name','sample_group','target_gene','barcode','fwd_primer','rev_primer','file1','file2'])
     outfile.write(header + "\n")
 
diff --git a/pipeline/make.py b/pipeline/make.py
deleted file mode 100644
index c69ef0d68..000000000
--- a/pipeline/make.py
+++ /dev/null
@@ -1,98 +0,0 @@
-import django
-from django.conf import settings
-from django.template.loader import get_template
-import sys, os, json, hjson
-
-
-def path_join(*args):
-    return os.path.abspath(os.path.join(*args))
-
-
-CURR_DIR = os.path.dirname(os.path.realpath(__file__))
-TEMPLATE_DIR = CURR_DIR
-#TEMPLATE_DIR = path_join(CURR_DIR, "templates")
-
-
-def set_env():
-    '''
-    Specify template engine and template directory.
-    Pass the settings variable to configure.
-    '''
-
-    TEMPLATES = [
-        {
-            'BACKEND': 'django.template.backends.django.DjangoTemplates',
-            'DIRS': [TEMPLATE_DIR],
-        }
-    ]
-    settings.configure(TEMPLATES=TEMPLATES)
-    return
-
-
-def render(data, template):
-    set_env()
-    django.setup()
-    temp = get_template(template)
-    html = temp.render(data)
-    return html
-
-
-def name_val_pair(element):
-    '''
-    input is a dictionary object and it returns a name, value pair.
-    '''
-
-    try:
-        value = element['default'] if not element['value'] else element['value']
-    except KeyError:
-        print("{0} raises an error".format(element['name']) )
-    return element['name'], value
-
-
-def parse_configs(configs):
-    '''
-    parse config file and returns a dictionary to be rendered.
-    '''
-
-    specs = dict()
-    for element in configs:
-        if not element['name'] == "analysis_spec":
-            name, value = name_val_pair(element)
-            specs[name] = value
-    return specs
-
-
-def load_specs(fname):
-    try:
-        data = open(fname).read()
-    except OSError as e:
-        print("File not found: {0}".format(e))
-        sys.stderr.close()
-    #data = json.loads(data)
-    data = hjson.loads(data)
-    return data
-
-
-def run():
-    config = sys.argv[1]
-    template = sys.argv[2]
-
-    #config = "./templates/metabarcode_qc/metabarcode_spec.hjson"
-    #template = "./templates/metabarcode_qc/metabarcode_makefile.html"
-
-
-    # loads sepc file.
-    configs = load_specs(config)
-
-    # parse configs to render in template.
-    specs = parse_configs(configs)
-
-    context = {'specs': specs, 'jobid': 'job0' }
-
-    # render template.
-    html = render(context, template)
-    print(html)
-
-
-if __name__ == "__main__":
-    run()
diff --git a/pipeline/qc/__init__.py b/pipeline/qc/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/pipeline/qc/qc_spec.hjson b/pipeline/qc/qc_spec.hjson
new file mode 100644
index 000000000..b66ae7547
--- /dev/null
+++ b/pipeline/qc/qc_spec.hjson
@@ -0,0 +1,124 @@
+{
+sampleinfo :
+    {
+    value : ~/tmp/sampleinfo.txt
+    help :
+           '''
+Enter a tab delimited text file. Order of the fields should be
+sample name, sample group, barcode, forward primer sequence, reverse primer sequence, target gene.
+Sample name should match the sample name in the dataset.
+    '''
+    label : Specify the sample file.
+    css: red
+    visible: 1
+    display_type: UPLOAD
+    }
+data :
+  {
+    value: ~/tmp/data.tar.gz
+    visible: 1
+    origin: PROJECT
+    data_type: TAR_FASTQ_GZ
+    display_type: DROPDOWN
+
+  }
+library_type :
+  {
+    value : true
+    label : Data entered is paired end.
+    visible: 1
+    display_type: CHECKBOX
+  }
+trim_primer:
+ {
+    label : Trims barcode and primer sequences.
+    value : true
+    help : Barcode and primer sequences should be in the sample sheet.
+    visible: 1
+    display_type: CHECKBOX
+
+ }
+trim_quality:
+ {
+
+    label : Specify average quality value for trimming.
+    help : Leave empty for not trimming
+    value :  30
+    range  : [20,32]
+    visible : 1
+    display_type : INTEGER
+ }
+merge_mismatch:
+  {
+  label : Maximum mismatch allowed. Default is 3.0.
+  value : 3.0
+  range : [0.9,5.1]
+  visible : 1
+  display_type : FLOAT
+  }
+merge_overlap:
+  {
+  label : Minimum number of overlapping bases to allow merging. Default is 12.
+  value :12
+  range : [8,16]
+  visible : 1
+  display_type : INTEGER
+  }
+action :
+ {
+    choices : {
+            fastqc : Create fastqc report
+            merge : Merge paired end dataset
+               }
+
+    value : merge
+    visible : 1
+    display_type: RADIO
+  }
+  // scripts info
+input_check :
+  {
+
+    value : ../../check_input.py
+    display_type : SCRIPT
+  }
+report_template :
+  {
+     value : metabarcode_report.html
+     display_type : SCRIPT
+  }
+report_script :
+  {
+     value : metabarcode_results.py
+     display_type: SCRIPT
+  }
+analysis_spec :
+  {
+    value: Quality control of sequencing data
+    description:
+                '''
+# Purpose
+
+This analysis takes a pired end dataset and produces a merged improved dataset.
+It can optionally trimmed the data before merging.
+MultiQC quality reports of each step are also produced.
+
+# Parameters
+
+**Input:**
+
+1. Paired end sequence data as a  tar archived gzip file.
+2. Sample information sheet as a tab delimited text file.
+
+# Results
+
+This analysis produces
+
+1. MultiQC report - an aggregate fastqc report of the input data.
+2. Trimmed dataset and its quality report (optional).
+3. Merged dataset and its quality report.
+
+        '''
+       display_type:MODEL
+  }
+}
diff --git a/pipeline/qc/templates/qc_makefile.html b/pipeline/qc/templates/qc_makefile.html
new file mode 100644
index 000000000..555125dbe
--- /dev/null
+++ b/pipeline/qc/templates/qc_makefile.html
@@ -0,0 +1,96 @@
+
+INPUT_DATA = {{data.value}}
+INPUT_SAMPLE_INFO := {{sampleinfo.value}}
+
+
+#
+# Internal parameters after this.
+#
+
+DATA_DIR = data
+RESULT_DIR  = results
+
+PTRIM_DIR = $(DATA_DIR)/trim/trimp
+QTRIM_DIR = $(DATA_DIR)/trim/trimq
+UPDATED_SAMPLE_INFO = updated_sampleinfo.txt
+
+UNPACKED_FASTQ = $(DATA_DIR)/*.fastq.gz
+FASTQC_REPORT = $(DATA_DIR)/*_fastqc.html
+TRIMMED_PRIMER = $(PTRIM_DIR)/*.gz
+TRIMMED_QUALITY =$(QTRIM_DIR)/*.gz
+
+all: $(FASTQC_REPORT) $(TRIMMED_QUALITY)
+	@echo "executes all commands"
+
+$(UNPACKED_FASTQ): $(INPUT_DATA)
+	tar -xzvmf $(INPUT_DATA)
+
+$(FASTQC_REPORT): $(UNPACKED_FASTQ)
+	ls $(DATA_DIR)/*.gz | parallel --verbose --progress -j 8 fastqc --nogroup {} -o $(DATA_DIR)
+
+ERR_LOG = stderr.txt
+
+$(UPDATED_SAMPLE_INFO): $(INPUT_SAMPLE_INFO)
+	#	
+	# Make new sample sheet named $(UPDATED_SAMPLE_INFO)
+	#
+	python -m pipeline.data.samplesheet $(INPUT_SAMPLE_INFO) $(DATA_DIR) > $(UPDATED_SAMPLE_INFO)
+
+
+multiqc: fastqc $(RESDIR)
+	#
+	# run multiqc to create an aggregate report
+	#
+	mkdir -p $(RESDIR)
+	multiqc -f -n input_multiqc -o $(DATADIR) $(DATADIR)
+	cp $(DATADIR)/input_multiqc.html $(RESDIR)
+	#
+	# clean
+	#
+	#rm -f $(DATADIR)/*fastqc.zip
+
+$(TRIMMED_PRIMER): $(UPDATED_SAMPLE_INFO) $(INPUT_DATA)
+	#
+	mkdir -p $(PTRIM_DIR)/logs
+	#
+	#
+	# trim left primer
+	mkdir -p $(RESULT_DIR)
+	cat $(UPDATED_SAMPLE_INFO) |parallel --verbose --progress  --header : --colsep '\t' bbduk.sh \
+	in1=$(DATA_DIR)/{file1} in2=$(DATA_DIR)/{file2} \
+	out1=$(PTRIM_DIR)/{sample_name}_fwd1_trim.fq.gz \
+	out2=$(PTRIM_DIR)/{sample_name}_fwd2_trim.fq.gz \
+	literal={barcode}{fwd_primer} ktrim=l k=23 hdist=1 tpe tbo overwrite=true \
+	overwrite=t skipr2=t stats=$(PTRIM_DIR)/logs/{sample_name}_fwd_stats.txt
+
+	#
+	# trim right primer
+	#
+	cat $(UPDATED_SAMPLE_INFO) | parallel --verbose --progress --header : --colsep '\t' bbduk.sh  \
+	in1=$(PTRIM_DIR)/{sample_name}_fwd1_trim.fq.gz \
+	in2=$(PTRIM_DIR)/{sample_name}_fwd2_trim.fq.gz \
+	out1=$(PTRIM_DIR)/{sample_name}_R1_trimp.fq.gz \
+	out2=$(PTRIM_DIR)/{sample_name}_R2_trimp.fq.gz  \
+	literal={barcode}{rev_primer} ktrim=l k=28 hdist=1 tpe tbo overwrite=true \
+	skipr1=t stats=$(PTRIM_DIR)/logs/{sample_name}_rev_stats.txt
+	#
+	# clean
+	#
+	cat $(PTRIM_DIR)/logs/*stats.txt > $(RESULT_DIR)/trimp_stats.txt
+	#rm -f $(PTRIM_DIR)/*trimfwd*
+
+
+$(TRIMMED_QUALITY): $(TRIMMED_PRIMER)
+	mkdir -p $(QTRIM_DIR)/logs
+	cat  $(UPDATED_SAMPLE_INFO) |parallel --verbose --progress  --header : --colsep '\t' bbduk.sh \
+	in1=$(PTRIM_DIR)/{sample_name}_R1_trimp.fq.gz in2=$(PTRIM_DIR)/{sample_name}_R2_trimp.fq.gz \
+	qtrim=rl trimq={{trim_quality.value}}  minlength=35 overwrite=true \
+	out1=$(QTRIM_DIR)/{sample_name}_R1_trim.fq.gz \
+	out2=$(QTRIM_DIR)/{sample_name}_R2_trim.fq.gz stats=$(QTRIM_DIR)/logs/{sample_name}_stats.txt
+	cat $(QTRIM_DIR)/logs/*stats.txt > $(RESULT_DIR)/trimq_stats.txt
+	#
+	# quality report
+	#
+	ls $(QTRIM_DIR)/*gz | parallel --verbose --progress -j 8 fastqc --nogroup {} -o $(QTRIM_DIR)
+	multiqc -n trim_multiqc --force -o $(QTRIM_DIR) $(QTRIM_DIR)
+	cp $(QTRIM_DIR)/trim_multiqc.html $(RESULT_DIR)
diff --git a/pipeline/qc/test.py b/pipeline/qc/test.py
new file mode 100644
index 000000000..86a8517b7
--- /dev/null
+++ b/pipeline/qc/test.py
@@ -0,0 +1,15 @@
+from pipeline import render
+
+import os
+
+CURR_DIR = os.path.dirname(os.path.realpath(__file__))
+
+TEMPLATE_FILE= os.path.join(CURR_DIR, 'templates', 'qc_makefile.html')
+SPEC_FILE = os.path.join(CURR_DIR, 'qc_spec.hjson' )
+
+if __name__ =="__main__":
+    spec = open(SPEC_FILE).read()
+    tmpl = open(TEMPLATE_FILE).read()
+    html = render.render_string(spec, tmpl)
+    print(html)
+
diff --git a/pipeline/render.py b/pipeline/render.py
new file mode 100644
index 000000000..214c77d99
--- /dev/null
+++ b/pipeline/render.py
@@ -0,0 +1,56 @@
+import django
+from django.conf import settings
+from django.template.loader import get_template
+from django.template import Template,Context
+import os, hjson
+
+
+def set_env():
+    '''
+    Specify template engine and template directory.
+    Pass the settings variable to configure.
+    '''
+
+    TEMPLATES = [
+        {
+            'BACKEND': 'django.template.backends.django.DjangoTemplates',
+            'DIRS': 'foo',
+            'OPTIONS': {
+                'string_if_invalid': "***MISSING**"
+            },
+        }
+    ]
+    settings.configure(TEMPLATES=TEMPLATES)
+    django.setup()
+    return
+
+
+def render_file(data, template_file):
+    template_txt = open(template_file).read()
+    return render_string(data, template_txt)
+
+
+def render_string(data, template_txt):
+    set_env()
+
+    spec = hjson.loads(data)
+
+
+    template = Template(template_txt)
+    context = Context(spec)
+    html = template.render(context)
+    return html
+
+
+if __name__ == "__main__":
+
+    config = "./templates/metabarcode_qc/metabarcode_spec.hjson"
+    template = "./templates/metabarcode_qc/metabarcode_makefile.html"
+
+    html = render_file(config, template)
+    print(html)
+
+
+
+
+
diff --git a/pipeline/run_job.py b/pipeline/run_job.py
index 053a8d77e..a5ece4c67 100644
--- a/pipeline/run_job.py
+++ b/pipeline/run_job.py
@@ -1,67 +1,99 @@
 import subprocess, os
-import urllib.request
-#from engine.models import Job
+import sys, json, hjson
+from pipeline.render import render_file,render_string
 
-
-DATA="http://iris.bx.psu.edu/projects/metabarcode-data/data.tar.gz"
-SINFO="http://iris.bx.psu.edu/projects/metabarcode-data/sampleinfo.txt"
+CURR_DIR = os.path.dirname(os.path.realpath(__file__))
 
 
 def run(job):
-    '''
+    ''''
     takes job object, runs the job and return job status
     '''
 
     spec = job.spec
     template = job.template
     outdir = job.outdir
-    jobid = job.jobid
-
-    # create Makefile for analysis
-    process1 = subprocess.run(['python','make.py', spec,template], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    print(process1.check_returncode())
-    
-    if not os.path.exists(outdir):
-            os.system('mkdir -p  {0}'.format(outdir))
-
-    mfile = open(os.path.join(outdir, "Makefile"), "w")
-    mfile.write(process1.stdout.decode('utf-8'))
-    mfile.close()
-
-    # get analysis data
-    urllib.request.urlretrieve(SINFO, os.path.join(outdir, 'sampleinfo.txt'))
-    urllib.request.urlretrieve(DATA, os.path.join(outdir, 'data.tar.gz'))
-    
-    # run analysis
-    process2 = subprocess.run(['make', 'all'], cwd=outdir)
-    print(process2.check_returncode())
-    
-    print("{0} ran successfully!".format(jobid))
-    return
+    #jobid = job.jobid
 
+    errorlog = []
 
-class Job:
-    pass
+    try:
 
+        mtext = render_string(spec,template)
 
-if __name__ == "__main__":
+        if not os.path.isdir(outdir):
+            os.mkdir(outdir)
+
+        with open(os.path.join(outdir, "Makefile"), 'wt') as fp:
+            fp.write(mtext)
+
+        process = subprocess.run(['make', 'all'], cwd=outdir, stderr=subprocess.PIPE, check=True)
+        job.status = process.returncode
+
+    except subprocess.CalledProcessError as err:
+        print("ERROR!!")
+        errorlog.append(err.stderr.decode('utf-8'))
+        print("***",err.returncode)
+        job.status = err.returncode
+
+    finally:
+        print(CURR_DIR)
+        #errorlog.append(process.stderr.decode('utf-8'))
+        job.log = "\n".join(errorlog)
+        print("printing errlog")
+        print(job.log)
+        #job.save()
+        #print("Job Done")
+
+    return job
+
+
+def get_spec(specfile='spec'):
+    spec = hjson.load(open(specfile))
+    return spec
+
+
+def test_job(data='data', sinfo='sinfo'):
+
+    spec_file = "templates/qc/qc_spec.hjson"
+    template_file = "templates/qc/qc_makefile.html"
 
-    # these won't be needed later.
-    ############# 
-    spec = "templates/metabarcode_qc/metabarcode_spec.hjson"
-    template = "templates/metabarcode_qc/metabarcode_makefile.html"
-    out = "./workout"
-    jobid = "job0"
+
+    spec = get_spec(specfile=spec_file)
+
+    spec['data']['value'] = data
+    spec['sampleinfo']['value'] = sinfo
+
+    new_spec = hjson.dumps(spec)
+    template_txt = open(template_file).read()
+
+    #html=render_string(new_spec,template_txt)
+    #print(html)
+    #1/0
 
     job = Job()
-    job.jobid= jobid
-    job.spec = spec
-    job.template = template
-    job.outdir = out
-    ##########
+    job.jobid= "job0"
+    job.spec = new_spec
+    job.template = template_txt
+    job.outdir = "./work"
+    job.status =""
+
 
     run(job)
 
+    print (job.status)
+    print (job.log)
+
+
+class Job:
+    pass
+
+
+if __name__ == "__main__":
+
+    test_job(data="~/work/web-dev/biostar-engine/pipeline/testdata/data.tar.gz",sinfo="~/work/web-dev/biostar-engine/pipeline/testdata/sampleinfo.txt")
+    #run(job)
+
 
 
 
diff --git a/pipeline/templates/qc/qc_makefile.html b/pipeline/templates/qc/qc_makefile.html
index 2e9846d3b..6a3e417e1 100644
--- a/pipeline/templates/qc/qc_makefile.html
+++ b/pipeline/templates/qc/qc_makefile.html
@@ -1,9 +1,8 @@
-JOBID = {{jobid}}
 DATADIR = data
 RESDIR  = results
 
-INPUTDATA = {{specs.data}}
-INPUT_SAMPLEINFO := {{specs.sampleinfo}}
+INPUTDATA = {{data.value}}
+INPUT_SAMPLEINFO = {{sampleinfo.value}}
 
 PTRIM_DIR = $(DATADIR)/trim/trimp
 QTRIM_DIR = $(DATADIR)/trim/trimq
@@ -32,13 +31,13 @@
 	#	
 	# Make new sample sheet named $(UPDATED_SAMPLE_SHEET)
 	#
-	python ../samplesheet.py $(INPUT_SAMPLEINFO) $(DATADIR) 2>>$(ERR_LOG)
+	python -m pipeline.qc.samplesheet.py $(INPUT_SAMPLEINFO) $(DATADIR)
 
 fastqc: extract
 	#
 	# run fastqc on all files
 	#
-	ls $(DATADIR)/*gz | parallel --verbose --progress -j 8 fastqc --nogroup {} -o $(DATADIR) 2>>$(ERR_LOG)
+	ls $(DATADIR)/*gz | parallel --verbose --progress -j 8 fastqc --nogroup {} -o $(DATADIR)
 
 multiqc: fastqc $(RESDIR)
 	#
@@ -63,7 +62,7 @@
 	out1=$(PTRIM_DIR)/{sample_name}_fwd1_trim.fq.gz \
 	out2=$(PTRIM_DIR)/{sample_name}_fwd2_trim.fq.gz \
 	literal={barcode}{fwd_primer} ktrim=l k=23 hdist=1 tpe tbo \
-	overwrite=t skipr2=t stats=$(PTRIM_DIR)/logs/{sample_name}_fwd_stats.txt 2>>$(ERR_LOG)
+	overwrite=t skipr2=t stats=$(PTRIM_DIR)/logs/{sample_name}_fwd_stats.txt
 
 	#
 	# trim right primer
@@ -74,7 +73,7 @@
 	out1=$(PTRIM_DIR)/{sample_name}_R1_trimp.fq.gz \
 	out2=$(PTRIM_DIR)/{sample_name}_R2_trimp.fq.gz  \
 	literal={barcode}{rev_primer} ktrim=l k=28 hdist=1 tpe tbo \
-	skipr1=t stats=$(PTRIM_DIR)/logs/{sample_name}_rev_stats.txt 2>>$(ERR_LOG)
+	skipr1=t stats=$(PTRIM_DIR)/logs/{sample_name}_rev_stats.txt
 	#
 	# clean
 	#
@@ -88,7 +87,7 @@
 	in1=$(PTRIM_DIR)/{sample_name}_R1_trimp.fq.gz in2=$(PTRIM_DIR)/{sample_name}_R2_trimp.fq.gz \
 	qtrim=rl trimq={{specs.trim_quality}}  minlength=35  \
 	out1=$(QTRIM_DIR)/{sample_name}_R1_trim.fq.gz \
-	out2=$(QTRIM_DIR)/{sample_name}_R2_trim.fq.gz stats=$(QTRIM_DIR)/logs/{sample_name}_stats.txt 2>>$(ERR_LOG)
+	out2=$(QTRIM_DIR)/{sample_name}_R2_trim.fq.gz stats=$(QTRIM_DIR)/logs/{sample_name}_stats.txt
 	cat $(QTRIM_DIR)/logs/*stats.txt > $(RESDIR)/trimq_stats.txt 
 	#
 	# quality report
diff --git a/pipeline/templates/qc/qc_spec.hjson b/pipeline/templates/qc/qc_spec.hjson
index 96533995f..9271137dd 100644
--- a/pipeline/templates/qc/qc_spec.hjson
+++ b/pipeline/templates/qc/qc_spec.hjson
@@ -1,7 +1,7 @@
 {
 sampleinfo :
     {
-    value : test/sampleinfo.txt
+    value : sampleinfo.txt
     help :
            '''
 Enter a tab delimited text file. Order of the fields should be
@@ -15,7 +15,7 @@ Sample name should match the sample name in the dataset.
     }
 data :
   {
-    value: test/data.tar.gz
+    value: data.tar.gz
     visible: 1
     origin: PROJECT
     data_type: TAR_FASTQ_GZ
@@ -121,4 +121,4 @@ This analysis produces
         '''
        display_type:MODEL
   }
-}
\ No newline at end of file
+}
diff --git a/setup.py b/setup.py
new file mode 100644
index 000000000..1fcae46cb
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,6 @@
+from setuptools import setup, find_packages
+setup(
+    name="Biostar Pipelines",
+    version="0.1",
+    packages= [ "pipeline" ],
+)