diff --git a/cmd/dump.go b/cmd/dump.go
index 3e1ccdb8a3..57f1113ea3 100644
--- a/cmd/dump.go
+++ b/cmd/dump.go
@@ -26,10 +26,14 @@ It can be used for backup and capture Gogs server image to send to maintainer`,
 	Action: runDump,
 	Flags: []cli.Flag{
 		cli.BoolFlag{"verbose, v", "show process details", ""},
+		cli.StringFlag{"config, c", "custom/conf/app.ini", "Configuration file", ""},
 	},
 }
 
 func runDump(ctx *cli.Context) {
+	if ctx.IsSet("config") {
+		setting.CustomConf = ctx.String("config")
+	}
 	setting.NewConfigContext()
 	models.LoadModelsConfig()
 	models.SetEngine()
diff --git a/cmd/serve.go b/cmd/serve.go
index 1f5d944d4f..af18e05c1e 100644
--- a/cmd/serve.go
+++ b/cmd/serve.go
@@ -27,7 +27,9 @@ var CmdServ = cli.Command{
 	Usage:       "This command should only be called by SSH shell",
 	Description: `Serv provide access auth for repositories`,
 	Action:      runServ,
-	Flags:       []cli.Flag{},
+	Flags: []cli.Flag{
+		cli.StringFlag{"config, c", "custom/conf/app.ini", "Configuration file", ""},
+	},
 }
 
 func setup(logPath string) {
@@ -83,6 +85,9 @@ func In(b string, sl map[string]models.AccessType) bool {
 }
 
 func runServ(k *cli.Context) {
+	if k.IsSet("config") {
+		setting.CustomConf = k.String("config")
+	}
 	setup("serv.log")
 
 	keys := strings.Split(os.Args[2], "-")
diff --git a/cmd/update.go b/cmd/update.go
index cc55693e2b..2ea7e942dd 100644
--- a/cmd/update.go
+++ b/cmd/update.go
@@ -11,6 +11,7 @@ import (
 
 	"github.com/gogits/gogs/models"
 	"github.com/gogits/gogs/modules/log"
+	"github.com/gogits/gogs/modules/setting"
 )
 
 var CmdUpdate = cli.Command{
@@ -18,10 +19,15 @@ var CmdUpdate = cli.Command{
 	Usage:       "This command should only be called by SSH shell",
 	Description: `Update get pushed info and insert into database`,
 	Action:      runUpdate,
-	Flags:       []cli.Flag{},
+	Flags: []cli.Flag{
+		cli.StringFlag{"config, c", "custom/conf/app.ini", "Configuration file", ""},
+	},
 }
 
 func runUpdate(c *cli.Context) {
+	if c.IsSet("config") {
+		setting.CustomConf = c.String("config")
+	}
 	cmd := os.Getenv("SSH_ORIGINAL_COMMAND")
 	if cmd == "" {
 		return
diff --git a/cmd/web.go b/cmd/web.go
index 55b6bf0874..ceb2134447 100644
--- a/cmd/web.go
+++ b/cmd/web.go
@@ -55,6 +55,7 @@ and it takes care of all the other things for you`,
 	Action: runWeb,
 	Flags: []cli.Flag{
 		cli.StringFlag{"port, p", "3000", "Temporary port number to prevent conflict", ""},
+		cli.StringFlag{"config, c", "custom/conf/app.ini", "Configuration file", ""},
 	},
 }
 
@@ -165,6 +166,9 @@ func newMacaron() *macaron.Macaron {
 }
 
 func runWeb(ctx *cli.Context) {
+	if ctx.IsSet("config") {
+		setting.CustomConf = ctx.String("config")
+	}
 	routers.GlobalInit()
 	checkVersion()
 
diff --git a/models/publickey.go b/models/publickey.go
index 67ab4242f2..893ff5c96a 100644
--- a/models/publickey.go
+++ b/models/publickey.go
@@ -29,7 +29,7 @@ import (
 
 const (
 	// "### autogenerated by gitgos, DO NOT EDIT\n"
-	_TPL_PUBLICK_KEY = `command="%s serv key-%d",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty %s` + "\n"
+	_TPL_PUBLICK_KEY = `command="%s serv --config=%s key-%d",no-port-forwarding,no-X11-forwarding,no-agent-forwarding,no-pty %s` + "\n"
 )
 
 var (
@@ -98,7 +98,7 @@ func (k *PublicKey) OmitEmail() string {
 
 // GetAuthorizedString generates and returns formatted public key string for authorized_keys file.
 func (key *PublicKey) GetAuthorizedString() string {
-	return fmt.Sprintf(_TPL_PUBLICK_KEY, appPath, key.Id, key.Content)
+	return fmt.Sprintf(_TPL_PUBLICK_KEY, appPath, setting.CustomConf, key.Id, key.Content)
 }
 
 var (
diff --git a/models/repo.go b/models/repo.go
index 3e07adba63..5a40c5b987 100644
--- a/models/repo.go
+++ b/models/repo.go
@@ -30,7 +30,7 @@ import (
 )
 
 const (
-	TPL_UPDATE_HOOK = "#!/usr/bin/env %s\n%s update $1 $2 $3\n"
+	TPL_UPDATE_HOOK = "#!/usr/bin/env %s\n%s update --config=%s $1 $2 $3\n"
 )
 
 var (
@@ -424,7 +424,7 @@ func initRepository(f string, u *User, repo *Repository, initReadme bool, repoLa
 
 	// hook/post-update
 	if err := createHookUpdate(filepath.Join(repoPath, "hooks", "update"),
-		fmt.Sprintf(TPL_UPDATE_HOOK, setting.ScriptType, "\""+appPath+"\"")); err != nil {
+		fmt.Sprintf(TPL_UPDATE_HOOK, setting.ScriptType, "\""+appPath+"\"", setting.CustomConf)); err != nil {
 		return err
 	}
 
diff --git a/modules/setting/setting.go b/modules/setting/setting.go
index 6a205921b8..f5212a2867 100644
--- a/modules/setting/setting.go
+++ b/modules/setting/setting.go
@@ -125,6 +125,7 @@ var (
 	Cfg          *ini.File
 	ConfRootPath string
 	CustomPath   string // Custom directory path.
+	CustomConf   string
 	ProdMode     bool
 	RunUser      string
 	IsWindows    bool
@@ -173,13 +174,16 @@ func NewConfigContext() {
 		CustomPath = path.Join(workDir, "custom")
 	}
 
-	cfgPath := path.Join(CustomPath, "conf/app.ini")
-	if com.IsFile(cfgPath) {
-		if err = Cfg.Append(cfgPath); err != nil {
-			log.Fatal(4, "Fail to load custom 'conf/app.ini': %v", err)
+	if len(CustomConf) == 0 {
+		CustomConf = path.Join(CustomPath, "conf/app.ini")
+	}
+
+	if com.IsFile(CustomConf) {
+		if err = Cfg.Append(CustomConf); err != nil {
+			log.Fatal(4, "Fail to load custom conf '%s': %v", CustomConf, err)
 		}
 	} else {
-		log.Warn("No custom 'conf/app.ini' found, ignore this if you're running first time")
+		log.Warn("Custom config (%s) not found, ignore this if you're running first time", CustomConf)
 	}
 	Cfg.NameMapper = ini.AllCapsUnderscore
 
diff --git a/routers/install.go b/routers/install.go
index 9c3f134d45..a3583a1a98 100644
--- a/routers/install.go
+++ b/routers/install.go
@@ -9,6 +9,7 @@ import (
 	"os"
 	"os/exec"
 	"path"
+	"path/filepath"
 	"strings"
 
 	"github.com/Unknwon/com"
@@ -221,8 +222,8 @@ func InstallPost(ctx *middleware.Context, form auth.InstallForm) {
 	cfg.Section("security").Key("INSTALL_LOCK").SetValue("true")
 	cfg.Section("security").Key("SECRET_KEY").SetValue(base.GetRandomString(15))
 
-	os.MkdirAll("custom/conf", os.ModePerm)
-	if err := cfg.SaveTo(path.Join(setting.CustomPath, "conf/app.ini")); err != nil {
+	os.MkdirAll(filepath.Dir(setting.CustomConf), os.ModePerm)
+	if err := cfg.SaveTo(setting.CustomConf); err != nil {
 		ctx.RenderWithErr(ctx.Tr("install.save_config_failed", err), INSTALL, &form)
 		return
 	}